[gmx-users] different results when using different number cpus
Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs on IBM cluster
Dear GMX users, I would like to give some feedback about my experience regarding the compilation of Gromacs 3.3.1 on the IBM cluster using the IBM compilers. Since I was unable to test a compilation with gcc, because gcc is not instaled, I've decided to recompile Gromacs with the IBM compilers using this this compilation script where I've disabled the optimizations for xlc_r and xlf_r. = export CC='xlc_r' export F77='xlf_r' export FFLAGS='-O0 -q64' export CFLAGS='-O0 -q64' export AR='ar -X 64' export LDFLAGS='-L/p5cecic/home/mretegan/software/fftw2_64/lib' export CPPFLAGS='-I/p5cecic/home/mretegan/software/fftw2_64/include' #export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' #export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' ./configure --enable-double --with-qmmm-cpmd --with-fft=fftw2 --prefix=/p5cecic/home/mretegan/software/gromacs_64_fftw2 With the new binaries I don't have problems when running grompp. Also I've also tested the binaries with the Gromacs tests found on the Wiki. All test have passed. So I think it's a good idea to disable all optimization when compiling on a IBM machine, and if everything runs smoothly start using optimizations for the compilers and test again. With respect Marius Retegan On Oct 31, 2007 4:36 PM, Marius Retegan [EMAIL PROTECTED] wrote: I have aprox. 81000 atoms. The system worked on a Itanium 2 cluster. On the IBM machine I've used the IBM compilers. I'm going to give it a try with gcc. Thank you Marius Retegan On 10/31/07, David van der Spoel [EMAIL PROTECTED] wrote: Marius Retegan wrote: 32 Gb on each node of the cluster. Maybe I should add that I've also ran CPMD and cp2k jobs on the cluster but I've never had memory problems. Marius Retegan It could still be too little, since this is the additional memory. What kind of system are you using, how many atoms? Does a small water box work? There have been problems with compilation on IBM machines as well, in particular when using IBM compilers. Recompiling with gcc resolves that. On 10/30/07, David van der Spoel [EMAIL PROTECTED] wrote: Marius Retegan wrote: Dear Gromacs users I'm having some troubles running grompp on a IBM cluster P575 with AIX 5.3 installed. This is the error message that I'm getting: processing coordinates... double-checking input for internal consistency... renumbering atomtypes... --- Program grompp_d, VERSION 3.3.1 Source code file: smalloc.c, line: 113 Fatal error: calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723) This says it wants one Gb of RAM. How much do you have? You can run grompp on a machine with a lot of memory and the mdrun on your cluster. --- I'm An Oakman (Pulp Fiction) : Not enough space While digging into the archive I've managed to find this post http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html, which basically says that there is not enough memory for the job. My job is lunched with LoadLeveler where I can define the @resources = ConsumableMemory (value), but if this is not defined in the LoadLeveler script, I think that the program should thake as much memory as it requires. So my question is why does Gromacs, a program renowned for low memory requirements, give this error message? Thank you Marius Retegan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read
Re: [gmx-users] different results when using different number cpus
Hi, With Gromacs and (nearly) all other MD packages you will never be able to get binary identical results when running on different number of CPUs. Since MD is chaotic, the results can be very different. Berk. From: Carsten Kutzner [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] different results when using different number cpus Date: Wed, 05 Dec 2007 14:10:06 +0100 Hi Dechang, it is normal that results are not binary identical if you compare the same MD system on different numbers of processors. If you use PME then you will probably get slightly different charge grids for 2 and for 16 processors - since the charge grid has to be divisible by the number of CPUs in x- and y-direction. Even if you manually set the grid dimensions to be the same for both cases, your simulations could diverge when using version 3.x of the FFTW. This version has a build-in timer and chooses the fastest of several algorithms which could be another even in two runs on the same number of processors - depending on the timing results. With different algorithms you get slight differences in the last digit of the computed numbers (rounding / truncation / order of evaluation) which will then grow during the simulation and lead to diverging trajectories. Of course the averaged properties of the simulation are unaffected by those differences and should be the same if averaged long enough. You could use FFTW 2.x and manually set the FFT grid size to the same value for the 2 and 16 CPU case - but I am not shure if this is enough to get binary identical results. You could also repeat your simulations several times with (slightly) different starting conditions (maybe different starting velocities) to get a better picture of the average behaviour of your system. If in all 16 processor cases you see the proteins diverge and in all 2 processor cases you see them converge, I would guess something is wrong. Hope that helps, Carsten Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =¡¡ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different results when using different number cpus
Message: 4 Date: Wed, 05 Dec 2007 14:19:28 +0100 From: Berk Hess [EMAIL PROTECTED] Subject: Re: [gmx-users] different results when using different number cpus To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; format=flowed Hi, With Gromacs and (nearly) all other MD packages you will never be able to get binary identical results when running on different number of CPUs. Since MD is chaotic, the results can be very different. Berk. I can confirm that I get the same thing when running a repeat of a simulation segment twice on 4 cpus with gromacs-3.3.1 and fftw-3.1.2. Further, while trying to debug a collegues parameters that give a lincs error after long periods of simulation time on a single processor I find that a proper restart from just prior to the crash does not lead to an exact repeat of the error (although an error does eventually occur). This was unfortunate since my plan was to save the .trr every 100ps and then do a restart in which I saved the .xtc every integration step to get a good look at the problem. Carsten's comments about fftw3.x is useful since I have been using fftw-3.1.2. Note that I did not test to see if a run on 1cpu will generate an identical trajectory, only that the lincs error is not exactly reproduced. I did the restart using .trr/.edr and set gen_vel=no;unconstrained_start=yes; for the restart. I agree that statistical properties will be properly reproduced, but I can imagine situations in which a proper restart would be identical: e.g. an interest in the dynamics of quick rare processes in which one might run for a long time while saving .xtc and .trr infrequently and then restarting at the proper place while saving .xtc very frequently in order to capture the dynamics of an identified transition. From: Carsten Kutzner [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] different results when using different number cpus Date: Wed, 05 Dec 2007 14:10:06 +0100 Hi Dechang, it is normal that results are not binary identical if you compare the same MD system on different numbers of processors. If you use PME then you will probably get slightly different charge grids for 2 and for 16 processors - since the charge grid has to be divisible by the number of CPUs in x- and y-direction. Even if you manually set the grid dimensions to be the same for both cases, your simulations could diverge when using version 3.x of the FFTW. This version has a build-in timer and chooses the fastest of several algorithms which could be another even in two runs on the same number of processors - depending on the timing results. With different algorithms you get slight differences in the last digit of the computed numbers (rounding / truncation / order of evaluation) which will then grow during the simulation and lead to diverging trajectories. Of course the averaged properties of the simulation are unaffected by those differences and should be the same if averaged long enough. You could use FFTW 2.x and manually set the FFT grid size to the same value for the 2 and 16 CPU case - but I am not shure if this is enough to get binary identical results. You could also repeat your simulations several times with (slightly) different starting conditions (maybe different starting velocities) to get a better picture of the average behaviour of your system. If in all 16 processor cases you see the proteins diverge and in all 2 processor cases you see them converge, I would guess something is wrong. Hope that helps, Carsten Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =¡¡ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: fullerene topology
I forgot to ask if there is a forcefield for gromacs that will handle fullerenes. Is there? -Adam On Dec 5, 2007 1:17 PM, Adam Fraser [EMAIL PROTECTED] wrote: I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files? If not, does anyone know of literature that would help me build C60? I already have a pdb of the structure... I just need accurate partial charges to build the topology file with. Even then, I'm not confident in how well this will model fullerene because I just read this: C60 has a tendency of avoiding having double bonds within the pentagonal rings which makes electron delocalisation poor, and results in the fact that C60 is not superaromatic. C60 behaves very much like an electron deficient alkene... source: http://www.ch.ic.ac.uk/local/projects/unwin/Fullerenes.html I greatly appreciate any help offered, thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Ambconv running
Hi, I am trying to use AMBCONV. However, it gives me a segmentation fault when I try to run it. I have seen that other users have posted a similar problem with the program on the mailing list. It seems to me that AMBCONV only uses older Amber formats. I have even generated that using set default oldprmtopformat on command. However I get the same segmentation fault. One user (David Evans) have mentioned that You can generate these from new format files using a utility in the amber package, but they will have an extra (7th) digit on the fouth line which will cause ambconv to crash. Does any one know what he means by the extra (7th) digit on the fourth line. Which file is he referring to ? The prmtop or the rst ? Any answers will be greatly appreciated. Best wishes Shozeb Haider The London School of Pharmacy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fullerene topology
I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files? If not, does anyone know of literature that would help me build C60? I already have a pdb of the structure... I just need accurate partial charges to build the topology file with. Even then, I'm not confident in how well this will model fullerene because I just read this: C60 has a tendency of avoiding having double bonds within the pentagonal rings which makes electron delocalisation poor, and results in the fact that C60 is not superaromatic. C60 behaves very much like an electron deficient alkene... source: http://www.ch.ic.ac.uk/local/projects/unwin/Fullerenes.html I greatly appreciate any help offered, thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] fullerene topology
Have you looked at the information / forcefields for carbon nanotubes? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Adam Fraser Sent: Thursday, 6 December 2007 5:17 AM To: Discussion list for GROMACS users Subject: [gmx-users] fullerene topology I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files? If not, does anyone know of literature that would help me build C60? I already have a pdb of the structure... I just need accurate partial charges to build the topology file with. Even then, I'm not confident in how well this will model fullerene because I just read this: C60 has a tendency of avoiding having double bonds within the pentagonal rings which makes electron delocalisation poor, and results in the fact that C60 is not superaromatic. C60 behaves very much like an electron deficient alkene... source: http://www.ch.ic.ac.uk/local/projects/unwin/Fullerenes.html I greatly appreciate any help offered, thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] different results when using different number cpus
Hi Dechang, it is normal that results are not binary identical if you compare the same MD system on different numbers of processors. If you use PME then you will probably get slightly different charge grids for 2 and for 16 processors - since the charge grid has to be divisible by the number of CPUs in x- and y-direction. Even if you manually set the grid dimensions to be the same for both cases, your simulations could diverge when using version 3.x of the FFTW. This version has a build-in timer and chooses the fastest of several algorithms which could be another even in two runs on the same number of processors - depending on the timing results. With different algorithms you get slight differences in the last digit of the computed numbers (rounding / truncation / order of evaluation) which will then grow during the simulation and lead to diverging trajectories. Of course the averaged properties of the simulation are unaffected by those differences and should be the same if averaged long enough. You could use FFTW 2.x and manually set the FFT grid size to the same value for the 2 and 16 CPU case - but I am not shure if this is enough to get binary identical results. You could also repeat your simulations several times with (slightly) different starting conditions (maybe different starting velocities) to get a better picture of the average behaviour of your system. If in all 16 processor cases you see the proteins diverge and in all 2 processor cases you see them converge, I would guess something is wrong. Hope that helps, Carsten Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Scaling Coulomb interactions with lambda, on a pair-wise basis
Hi, I am looking to scale non-bonded interactions between two atoms with the lambda parameter, while keeping other interactions unchanged. I am not sure how to do this for Coulomb interactions. Scaling the Lennard-Jones interactions between a specific atom pair seems straightforward, by setting VA, WA, VB, WB for that pair in the [PAIRS] directive. However, in order to modify Coulomb interactions between an atom pair, it seems I need to modify qA and qB for each atom -- this then affects the interactions between this atom and all other atoms as well, something I need to avoid. Is there a way to scale Coulomb interactions for a specific pair of atoms only? Thanks in advance -- Matt -- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ambconv running
you shall use AMBER's new2oldparm new old to get the old format file. I remember that David Mobley has another ambconv script on his website (http://www.alchemistry.org/) but it is not accessible right now. Regards, Yang Ye On 12/6/2007 3:52 AM, Shozeb Haider wrote: Hi, I am trying to use AMBCONV. However, it gives me a segmentation fault when I try to run it. I have seen that other users have posted a similar problem with the program on the mailing list. It seems to me that AMBCONV only uses older Amber formats. I have even generated that using set default oldprmtopformat on command. However I get the same segmentation fault. One user (David Evans) have mentioned that You can generate these from new format files using a utility in the amber package, but they will have an extra (7th) digit on the fouth line which will cause ambconv to crash. Does any one know what he means by the extra (7th) digit on the fourth line. Which file is he referring to ? The prmtop or the rst ? Any answers will be greatly appreciated. Best wishes Shozeb Haider The London School of Pharmacy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] different results when using different number cpus
1. how long is the simulation? 2. did you start from equilibration (with gen_vel=yes) or production md? 3. ... On 12/5/2007 8:28 PM, Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD using Gromacs
Thank you very much all for your consideration and fruitful advices. Regards, Monika On Wed, 2007-12-05 at 18:15 +1100, Mark Abraham wrote: Xavier Periole wrote: Dear Monika, the setup of a REMD simulation is actually quite straightforward. In the following I describe steps that would lead you to have a REMD simulation running on a given system. The success of the simulation will depend entirely on the problem you are addressing and the criterion you judge it. Although REMD simulation are helping in increasing sampling they do not provide the ultimate answer. This should be kept in mind. I've added a section on replica-exchange to http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation which people may wish to review. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 44, Issue 14
Hi, Mark You mean I should use gcc to compile the fftw, or both of fftw and gromacs? In fact I want to install a parellel gromacs, so perhaps I can install fftw with gcc, and install gromacs with xlc and mpcc? Thanks for your response. Li Zhenhai Department of Engineering Mechanics Tsinghua University Beijing 100084 China Tel: 86-10-62773779 E-mail: [EMAIL PROTECTED] 2007-12-06 Mark wrote: I'd suggest using gcc, or a gcc-compatibility mode of your compiler, if it exists. Mark -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] different results when using different number cpus
Yang Ye wrote: 1. how long is the simulation? 2. did you start from equilibration (with gen_vel=yes) or production md? 3. ... On 12/5/2007 8:28 PM, Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Answer is yes. http://wiki.gromacs.org/index.php/Reproducibility Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
