7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. 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. The simulations were not performed at constant velocity > but at constant force. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. PMID: 33550613 PMCID: PMC8089038 DOI: 10. edu> > wrote: > Roy, > > I think that you are confusing two things. 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). Maybe the file was not transferred correctly to your desktop PC. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. 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. INVENTING THE FUTURE OF MEDICINE. 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. 7b1 on NCSA. edu> wrote: > Roy, > > I think that you are confusing two things. by G. uiuc. Response Time: Within a few hours. Whitfield, 2 Esther Bullitt, 4 Ronald E. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. 10. I doubt that there is a way to have> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi > <gianluca_at_u. Facebook gives people the power to share and makes the world more open and connected. Gianluca Interlandi. unam. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. monu_at_gmail. Electrical Engineering. 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. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Semantic Scholar's Logo. washington. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. washington. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. 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:. 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. From: Gianluca Interlandi (gianluca_at_u. 7 ns/day, which seems decent given the system size. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. View all 11 amenities. washington. Just source the Tcl file and use the 'unwrap' procedure. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. washington. > > I have already run a bunch of pulling simulations in the NVE ensemble. uiuc. VMD-L Mailing List. washington. washington. 7 out the door on Friday. 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 > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. 7b1 - effects of configuration parameters and hardware. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Re: Help building a desktop for namd. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? Next in thread: Gianluca Interlandi: "Re: NAMD 2. 85. washington. 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)" From: Gianluca Interlandi (gianluca_at_u. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. 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. uiuc. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. washington. washington. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. 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. 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: Wed Oct 20 2010 - 15:33:33 CDT Next message: jnsong: "how to cenvert NAMD binary coordinate file to text file" Previous message: Jim Phillips: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Policies. Pavel Aprikian, # 1 Gianluca Interlandi, # 2 Brian A. washington. washington. Specifically, I’m testing different binding domains. 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. Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. washington. edu) Date: Tue Aug 04 2009 - 00:36:38 CDT Next message: Nicholas M Glykos: "Re: A script for performing calculations divided by quanta" Previous message: Joshua Adelman: "Re: A script for performing calculations divided by quanta". There have been over 180 downloads and no complaints so far. Balcony. From: Gianluca Interlandi (gianluca_at_u. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. Re: Langevin process in NAMD tutorial"Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. 7b1 on NCSA Abe. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. uiuc. Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. Hope the video helps, but now I'm embarrassed. The more tasks you have the > more frequently the CPUs need to update each other. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. Re: query about wrapped coordinates. 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. edu> wrote:Gianluca Interlandi. In the NAMD folder that you downloaded there >> is a file called "notes. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. txt". 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. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. The simulations were not performed at constant velocity > but at constant force. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. 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. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. Re: Help building a desktop for namd. washington. Here they are: a. washington. From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. 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. , "not (water or ions)" GianlucaRe: DCD. Gianluca Interlandi Research Assistant Professor. washington. Kitchen. You should simulate it in explicit water (or try one of the implicitIn reply to: Gianluca Interlandi: "What, if no temperatue control specified?" Messages sorted by: [ attachment ] Hi! A technical question. washington. washington. E-mail: [email protected],. washington. washington. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. washington. From: Mitchell Gleed (aliigleed16_at_gmail. Neil King Assistant Professor. washington. edu> Cc: <namd-l_at_ks. washington. 26588 Item in Clipboard Cite. washington. Bioengineering. edu> wrote: > Hi Fatemeh, > > Thanks for replying. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. 5923 Kcal/mol also we have 6. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. 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. 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. (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. 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). washington. washington. (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. washington. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. 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) 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. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. From: Gianluca Interlandi (gianluca_at_u. 2016. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. double. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message:. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). 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+). washington. I needed to install the 'patch' program. washington. Try copying it again from where the simulation was run. Re: Yet another NAMD speed concerns. Next in thread: Gianluca Interlandi: "Re: NAMD 2. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. washington. washington. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca 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 molecular. From: Gianluca Interlandi (gianluca_at_u. First of all, I am sorry to bother you again for problem. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. Re: Vibrational mode analysis. edu> > wrote: > are other people also using those GPUs? > > From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. Re: Vibrational mode analysis. , "not. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. Facebook gives people. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Just source the Tcl file and use the 'unwrap' procedure. These are the lastIn 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. 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). Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. NAMD doesn't that i know of. washington. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. 6 version, although I am not running the cluster at full load yet. edu) Date: Wed Dec 12 2012 - 14:49:46 CST Next message: JC Gumbart: "Re: NAMD and new FF CHARMM36" Previous message: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" In reply to: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" Next in thread: Jeffrey Potoff: "Re: NAMD and new FF CHARMM36" > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. But if you simulate entire proteins, charged termini. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. edu Search for more papers by this author> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. 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. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. com) Date: Wed Sep 18 2013 - 14:48:11 CDT Next message: Gianluca Interlandi: "Re: Open VMD from a remote host" Previous message: John Stone: "Re: Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Gianluca. 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. 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. washington. washington. at 298. Previous studies. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Re: Protein in/out of box. Neil King Assistant Professor. I doubt that there is a way to have NAMD output theFrom: Gianluca Interlandi (gianluca_at_u. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. Policies. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. washington. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. PMID: 37700555; DOI: 10. 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. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. From: Gianluca Interlandi (gianluca_at_u. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. washington. washington. > > I am trying to open VMD remotely. 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. There have been over 180 downloadsReply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. , and Thomas W. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. washington. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. washington. 7 out the door on Friday. washington. washington. washington. 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. washington. 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 smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. Author Profile. I needed to install the 'patch' program. washington. Gianluca 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. 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. uiuc. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. We are building a smaller cluster though in the lab and will test the scalabilityGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. Katrina T. From: Gianluca Interlandi (gianluca_at_u. Choose File -> Save Coordinates. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. washington. , Thomas W. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. Chemistry. washington. From: Gianluca Interlandi (gianluca_at_u. 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. Hope the video helps, but now I'm embarrassed. 1. Sarah Keller Professor. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. From: Gianluca Interlandi (gianluca_at_u. What this rental offers. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. It is experimentally knownReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. From: Mitchell Gleed (aliigleed16_at_gmail. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. edu> > wrote: > Roy, > > I think that you are confusing two things. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. From: Gianluca Interlandi [gianluca_at_u. washington. 7 released. washington. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. Gianluca Interlandi, Department of Bioengineering, University of Washington, Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. Contact host. washington. From: Gianluca Interlandi (gianluca_at_u. 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 smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Skip to search form Skip to main content Skip to account menu. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. From: Gianluca Interlandi (gianluca_at_u. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. Electrical. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. Corresponding Author:gianluca@u. I was recording the energies once every 100 steps. washington. From: Ernesto Vargas (vargaslo_at_gmail. Gianluca Interlandi. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. washington. washington. prm". washington. washington. edu) Date: Sat Jul 04 2015 - 15:33:25 CDT Next message: VINAYAK BHAT: "Generating solvent models. I wonder whether anybody > has had the same problem and found a solution. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. Eric Klavins Professor. 15 K 1 KT = 2. Anton. uiuc. washington. Sokurenko 1 , *. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. 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. 15 K 1 KT = 2. July; 84 (7):990–1008. 7 released" In reply to: Jim Phillips: "Re: NAMD 2. The only significant change since 2. 7b4 is thatRE: DCD. Rachel Klevit WRF Endowed Chair in Biochemistry. eduRe: Question about equilibration. unizh. From: John Stone (johns_at_ks. 100% refund of amount payable if you cancel at least 14 days before check-in. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu]Reply All Saturday,. Bathroom 1. washington. From: Gianluca Interlandi <gianluca_at_u. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. m. washington. washington. washington. That's why one wants to use a low value for the damping constant, in principle. g. From: Gianluca Interlandi (gianluca_at_u. 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. Languages: English, Spanish, Italian. You should simulate it in explicit water (or try one of the implicitOn 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+).