Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" Complex between VWF A1 and GpIbα and amino acid sequence of the A1 domain. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. washington. Chemistry. NAMD doesn't that i know of. washington. C; the more troublesome part is the lack of long-range electrostatic treatments. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. Gianluca has 2 jobs listed on their profile. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. Neil King Assistant Professor. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. Facebook gives people. 26588 Item in Clipboard Cite. Electrical Engineering. <br> <br>1999 March: Degree in modern languages result 107/110 - University of Catania, Italy with a degree thesis on Irish. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. Response Time: Within a few hours. From: Axel Kohlmeyer (akohlmey_at_gmail. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. washington. washington. From: Gianluca Interlandi [gianluca_at_u. SMD on center of mass. washington. Next in thread: Gianluca Interlandi: "Re: namd-l: DCD for windows" Messages sorted by: [ attachment ] Hi, We don't have a build of catdcd for windows currently, but it should be possible to make one. Sarah Keller Professor. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. I am > using the option "wrapAll on". edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. >From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. edu> wrote: > I would like to calculate the free energy of a protein-protein complex > using the Jarzinsky's equation from already performed SMD simulations. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. (did you see if any hunk failed?)Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. Deadline is this Friday (or in three > months). edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. washington. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Anton. From: Gianluca Interlandi (gianluca_at_u. Semantic Scholar's Logo. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. edu) Date: Wed Aug 05 2009 - 13:19:25 CDT Next message: Gianluca Interlandi: "Re: SMD output : which col represents force, second or last" Previous message: David Tanner: "Re: SMD output : which col represents force, second or last" In. uiuc. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Bidet · Toilet · Shower. washington. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. Fwd: Installing NAMD on windows. Electrical. AMBER does, and so does GROMACS. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. That's why one wants to use a low value for the damping constant, in principle. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. washington. washington. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. 7b1 - effects of configuration parameters and hardware. 7 out the door on Friday. That file contains information how to run >> NAMD (and also compile it. I empolyed PBC condition with wraping water and wraping all options on. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu>> > > I suspect that E3_19 might not be stable with this type of > implicit solvent model (it doesn't contain a term to take the > non-polar solvation energy into accout). edu > <mailto:gianluca_at_u. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. From: Gianluca Interlandi (gianluca_at_u. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. washington. From: Gianluca Interlandi (gianluca_at_u. I needed to install the 'patch' program. edu> > wrote: > Roy, > > I think that you are confusing two things. > > According to your banchmarks, it looks like the less expensive GTX285. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Languages spoken: English. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. 7 out the door on Friday. 5923 Kcal/mol also we have 6. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. From: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. washington. Sokurenko 1 , *. Just a good MD toy ! Victor owner-namd-l_at_ks. Re: external force. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. J. Justin Kollman Professor. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. Try copying it again from where the simulation was run. , and Thomas W. edu> Subject: Re: namd-l: "wrapAll on" with a complex Gianluca: Using VMD with the attached script should solve that. e. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Bioengineering. washington. I > attach a plot of a constant velocity simulation where I'm pulling two > proteins apart. edu> wrote: >> Hi! >> >> Are there any benchmarks available which compare the performance of NAMD on >> Lincoln (CUDA heterogenous cluster) with its performance on a traditionalVMD-L Mailing List. C; the more troublesome part is the lack of long-range electrostatic treatments. washington. >From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Hope the video helps, but now I'm embarrassed. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. uiuc. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. Re: Vibrational mode analysis. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu Search for more. by G. washington. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. Interlandi Mortgage Consultants, LLC Dec 2008 - Present 14 years 3 months. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. I have to run following commands 2 times in tcl. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. washington. Don't take my word that this works. From: Gianluca Interlandi (gianluca_at_u. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. Chemistry. monu_at_gmail. PMID: 37700555; DOI: 10. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Re: Help building a desktop for namd. I would be > happy if somebody could point me out to some scripts which help me performDCD. washington. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. washington. From: Gianluca Interlandi (gianluca_at_u. edu> wrote:Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. . At some point there will be a web page here. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. uiuc. 7 ns/day, which seems decent given the system size. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. Gianluca Interlandi. washington. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated le. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. edu) Date: Sat Jul 04 2015 - 15:33:25 CDT Next message: VINAYAK BHAT: "Generating solvent models. From: Victor Kwan (vkwan8_at_uwo. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. > > Forget about creating a pdb file. washington. washington. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. washington. washington. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. Friend and Aachal Jalan and Shivani Gupta and Gianluca Interlandi and Yan Liu* and Veronika Tchesnokova. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. I made those videos seven years ago. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. 15 K 1 KT = 2. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. > > I am trying to open VMD remotely. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. Languages: English, Spanish, Italian. washington. From: Gianluca Interlandi (gianluca_at_u. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. edu> wrote: > Roy, > > I think that you are confusing two things. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. washington. What this rental offers. edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. I was getting 2. From: Gianluca Interlandi (gianluca_at_u. I wonder whether anybody > has had the same problem and found a solution. Facebook gives people the power to share and makes the world more open and connected. washington. washington. I'm testing specifically this protein for its beaviour. From: Gianluca Interlandi (gianluca_at_u. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. washington. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. Neil King Assistant Professor. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. On Thu, Oct 20, 2011 at 05:48:32PM -0700, Gianluca Interlandi wrote: > Dear VMD users, > > A while ago I bothered this list asking for recommendations for a > lightweight laptop to buy which would support a decent 3D acceleration in > order to use VMD in presentations. In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. From: Gianluca Interlandi (gianluca_at_u. washington. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. From: Gianluca Interlandi (gianluca_at_u. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. washington. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Tue Oct 31 2023 - 21:41:13 CDT Next message: Vasista: "STRIDE breaks after 100,000 protein atoms" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA". edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. I would like to erase Windows and install Leap 42. 7 released. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. The difference is usually after the > 4th decimal after the period. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. Spaces. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. I wanted to briefly update here on my > experience. Jennifer KongRE: DCD. edu> > wrote: > Roy, > > I think that you are confusing two things. Write a review. Just a good MD toy ! Victor owner-namd-l_at_ks. View all 11 amenities. 6 ns/day for a 100k atom system with roughly those same parameters (and. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. washington. washington. eduRe: Question about equilibration. 5923 Kcal/mol also we have 6. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. washington. I needed to install the 'patch' program. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. washington. Gianluca Interlandi. Reply: Gianluca Interlandi: "Re: Regarding thermostats" Reply: Marcos Sotomayor: "Re: Regarding thermostats" Messages sorted by: [ attachment ] Dear NAMD users, Lately in the lab we have been discussing about which thermostat use in our simulations. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. washington. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Previous message: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" In reply to: Aron Broom: "Re: Am I doing the Right Thing?" Next in thread: Aron Broom: "Re: Am I doing the Right Thing?" Reply: Aron Broom: "Re: Am I doing the Right Thing?" Messages sorted by: [ attachment ] Hi Aron, I understand now what you are. washington. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. uiuc. washington. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. C; the more troublesome part is the lack of long-range electrostatic treatments. washington. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. edu> > wrote:From: Gianluca Interlandi [gianluca_at_u. From: Victor (ovchinnv_at_gmx. washington. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. washington. Re: Protein in/out of box. Re: Abe versus Lincoln. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. Previous message: Gianluca Interlandi: "NAMD 2. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. 6 version, although I am not running the cluster at full load yet. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. washington. washington. From: Gianluca Interlandi (gianluca_at_u. washington. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorGianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by. What can be the possible cause for this or does it happens naturally> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. rtf" and "par_all36_prot. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu on behalf of Gianluca Interlandi [gianluca_at_u. washington. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Both > simulations were started from X-ray structures. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. Michel Espinoza-Fonseca: "Re: Vibrational. edu> wrote: > I'm cc'ing here the NAMD list so that others. Here they are: a. VMD-L Mailing List. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. Maybe the file was not transferred correctly to your desktop PC. washington. washington. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. washington. 10. 100% refund of amount payable if you cancel at least 14 days before check-in. Katrina T. From: Gianluca Interlandi (gianluca_at_u. Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Previous studies. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. From: Gianluca Interlandi (gianluca_at_u. From: John Stone (johns_at_ks. I'm testing specifically this protein for its beaviour. In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Just source the Tcl file and use the 'unwrap' procedure. washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. washington. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. washington. washington. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. m. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. washington. washington. edu) Date: Tue Oct 17 2006 - 00:36:56 CDT Next message: Jacob Poehlsgaard: "Intel Woodcrest version?" Previous message: Jim Phillips: "Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006" In reply to: Gianluca Interlandi: "SMD and restart"> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. washington. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. 50% refund of amount payable if you cancel at least 7 days before check-in. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. washington. Kid friendly. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Re: Langevin damping coefficient.