Re: [gmx-users] gromacs installation on Vista
maryam zargarzadeh wrote: I would like to know if I can install gromax on vista and the procedure. Start by searching the GROMACS webpage. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization
subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ;Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force = 3.7720719e+04 on atom 5530 Norm of force = 1.7014005e+02 - Can anybody suggest what changes I can make Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reproducing Chain Tilt on DPPC gel phase with Martini FF
On Dec 9, 2009, at 11:21 PM, César Ávila wrote: Dear all, I would like to simulate a DPPC membrane in gel phase using Martini Force Field. As stated on Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model, CPL 135 (2005) 223-244 the correct 30º angle chain tilt for DPPC might be reproduced by reducing the acyl chain spheres volume by 10%. So far, I have tried changing sigma and epsilon for C1-C1 pair interaction without success. The sphere volume or radius is defined by sigma. Epsilon deals with the strength of the interactions; you do not want to modify it. Did you try to contact the authors? They might be of better help! Best regards Cesar Avila -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization
Hello Can increase the emtol from 1000 to 1 KJ mol - 1 nm-1? subarna From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, 10 December, 2009 2:33:23 PM Subject: Re: [gmx-users] energy minimization subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force = 3.7720719e+04 on atom 5530 Norm of force = 1.7014005e+02 - Can anybody suggest what changes I can make Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to plot free enenrgy landscape and exact corresponding conformation
Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation? Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to plot free enenrgy landscape and exact corresponding conformation
On 12/10/09 11:11 AM, xi zhao wrote: 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation? g_sham Thank you very much! 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization
subarna thakur wrote: Hello Can increase the emtol from 1000 to 1 KJ mol ^- 1 nm^-1? I wouldn't recommend it. That would be a really large maximum force, which would probably cause your system to be very unstable. Look at your original structure to see what might be wrong instead of just trying to find a way to push forward. -Justin ^ ^subarna *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, 10 December, 2009 2:33:23 PM *Subject:* Re: [gmx-users] energy minimization subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp= /usr/bin/cpp define = -DFLEX_SPC constraints= none integrator = steep nsteps = 3000 ; ;Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm= 1 ns_type= grid rlist = 1 coulombtype= PME rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel= no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force= 3.7720719e+04 on atom 5530 Norm of force= 1.7014005e+02 - Can anybody suggest what changes I can make Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://in.mg50.mail.yahoo.com/dc/mailto%3A%25e%25 http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists..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 gmx-users-requ...@gromacs.org http://in.mg50.mail.yahoo.com/dc/mailto%3A%25e%25. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New to Gromacs -- looking for insights
Thanks for the help. On 12/09/2009 05:57 PM, Mark Abraham wrote: Simone Pellegrini wrote: Dear all, I am researching optimization for MPI parallel programs. As I saw Gromacs seems to use MPI and my idea is to test some of the program transformations I am aware of to improve the performance. It's already fairly good - be sure to read the GROMACS 4 paper. Up to about 64 processors on good network hardware, GROMACS runs are usually quite CPU-bound, so it is not a good candidate for improvement through any MPI optimization. Probably it's working fine with the current MPI standards, but you know, MPI is evolving and some new features will be introduced in MPI 3 and I want to test if gromacs can take advantage of it. :) The MPMD communication pattern with PME at high parallelism is interesting, though, and might benefit from task layout that is cunning with respect to the network topology. The main problem is how should I get started with Gromacs? :) Which of the provided programs rely on MPI calls? and furthermore, where can I find some significant input files? Only mdrun uses MPI. Look on the web or the GROMACS wiki for some pointers to tutorials to learn how to construct a workflow that will lead to a meaningful test. thanks, I found a couple of mdb files on line and I am learning from it. Is there any repository with come real world example using gromacs 4? I found some benchmarks based on gromacs 3 and only half of them seem to work with the new gromacs. Mark thanks again for the support, regards S. Pellegrini -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to increase nodes in mdrun option
Mahendran E wrote: hi all while running gromacs in parallel environment i am getting the following command, the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error: Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5873 Fatal error: There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition --- Everybody Wants to Be Naked and Famous (Tricky) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 5 gcq#130: Everybody Wants to Be Naked and Famous (Tricky) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_16810: p4_error: : -1 p4_error: latest msg from perror: No such file or directory how to increase the nodes in mdrun option You are specifying 5 nodes with mpirun -np 5 ... so just change the number passed to the -np flag. -Justin thanks in advance Regards Mahendran.E -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to increase nodes in mdrun option
Mahendran E ha scritto: hi all while running gromacs in parallel environment i am getting the following command, the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error: Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5873 Fatal error: There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition --- Everybody Wants to Be Naked and Famous (Tricky) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 5 gcq#130: Everybody Wants to Be Naked and Famous (Tricky) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_16810: p4_error: : -1 p4_error: latest msg from perror: No such file or directory how to increase the nodes in mdrun option Increasing the number after mpirun -np , I'd say. m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to increase nodes in mdrun option
hi all while running gromacs in parallel environment *mpirun -np 3* -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr *for mpirun 3 nodes i got the output,* while trying to increase the nodes to 5 or 8 i am getting the following error the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error: Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5873 Fatal error: There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition --- Everybody Wants to Be Naked and Famous (Tricky) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 5 gcq#130: Everybody Wants to Be Naked and Famous (Tricky) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_16810: p4_error: : -1 p4_error: latest msg from perror: No such file or directory how to increase the nodes in mdrun option thanks in advance Regards Mahendran.E -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to increase nodes in mdrun option
Mahendran E wrote: hi all while running gromacs in parallel environment *mpirun -np 3* -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr *for mpirun 3 nodes i got the output,* while trying to increase the nodes to 5 or 8 i am getting the following error the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error: Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5873 Fatal error: There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition --- Have you followed this advice? There is a minimum size requirement for DD cells based on the cutoffs used, etc. You can alter these parameters by using the mdrun options that have been spelled out for you. If this does not work, then your system is simply too small to be split over more than a small amount of processors. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some questions about umbrella sampling
Dear All: I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce enough overlap to reduce WHAM errors, But I'm wondering how much overlap are reasonable overlap?Does there any rules I can use to judge whether my overlap is enough? My second question is that, how to choose number of bins, when I using g_wham command? Does it decided by the numbers of windows I used? I found that, different numbers will produce slightly different results (a difference of 0.5kcal/mol in my condition). What does it mean? Does it mean that, my simulation is not enough? the third question: I found someone say that, to get results in a good quality, one must make sure that, individual histograms should look smooth. What does it mean? Does it mean that,the distribution of the positions of the drug in one window should be smooth or should opproximately be an Gauss distribution(I found that, whether it is smooth is decided by the number of bins, if a very large number of bins is used, it is not smooth)? The last question: if my simulation produced enough overlap, can I believe that, my simulation is right theoretically? Thanks in advance!!! R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some questions about umbrella sampling
I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. why not gmx 4? In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce enough overlap to reduce WHAM errors, But I'm wondering how much overlap are reasonable overlap?Does there any rules I can use to judge whether my overlap is enough? I aim for 20%, but that's because I also conduct REMD-like exchanges. To be sure, you can do twice as many (or otherwise increase the overlap) and if the profile doesn't change then you had enough to begin with. I realize that this isn't a fantastically efficient solution, but I don't know of a better one. My second question is that, how to choose number of bins, when I using g_wham command? Does it decided by the numbers of windows I used? I found that, different numbers will produce slightly different results (a difference of 0.5kcal/mol in my condition). What does it mean? Does it mean that, my simulation is not enough? It could mean a lot of things. Based on what you mention below, I suspect that you are using too bins that are too small when the energy changes. WHAM works with probability histograms, and so you need enough counts per bin that if you were to run the entire simulation again the difference would be a small fraction of the average. the third question: I found someone say that, to get results in a good quality, one must make sure that, individual histograms should look smooth. What does it mean? Does it mean that,the distribution of the positions of the drug in one window should be smooth Yes or should opproximately be an Gauss distribution No. They could easily be bimodal. (I found that, whether it is smooth is decided by the number of bins, if a very large number of bins is used, it is not smooth)? See my comment above regarding probability histograms The last question: if my simulation produced enough overlap, can I believe that, my simulation is right theoretically? No. Your sampling within one or many or all umbrellas could still be trapped -- hence the reason that I do equilibrium exchange. Consider this: |-- Sidechain A | ---| drug in umbrella N versus: ---| drug in umbrella N | |-- Sidechain A Regular US does not offer an efficient mechanism for the sidechain A to switch sides of the drug while the drug is restrained to a given position when the drug is blocking the rotamerization of that sidechain. Allowing the constituent ensembles to interconvert using e.g. REMD alleviated this sampling deficiency. Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_velacc problem
Hi all, I am trying to do velocity auto-correlation function(VACF) for the 'oxygen atom' present in a 63 Ang. cubic water box, simulated upto 500ps. And the velocities are stored at every 5fs. While doing the analysis(g_velacc), it got struck at 400ps, since if felt it is mainly due to the memory problem, i redid my simulation by storing the velocities at every 7fs. Now the analysis went upto 497ps and got struck after that. I tried to truncate my trajectory upto 497 by using the -trunc option from trjconv command but again i faced the same problem as before while doing analysis. Can any one help how i go about it to succeed in doing VACF. Thank you. Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpispawn.c:303 Unexpected exit status
Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching the error message with this email. Have a look at it. If you need any more information let me know. Thanks for your help. Regards Shivkumar On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: You haven't addressed any of the comments or questions I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html When asking for free help, demonstrate that you're willing to take the advice you're given, and if that fails, state what problems remain. Otherwise, it seems like you're ignoring viable suggestions. For the sake of being explicit: your .mdp file is wrong, and the dynamics are likely spurious. Solve these issues (which I have described for you!) before moving to a more peripherally-related solution. Also check the .log file; as I said before, Gromacs rarely exits without offering its own error messages about what's going wrong. There is nothing in this output that immediately suggests your PME spacing is remotely at fault, but other parameters in your .mdp file are clearly wrong. -Justin shivkumar bale wrote: Hi Gromacs Users, The error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Following is the link which might help: http://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/%7Eetanner/MPI.htmlhttp://www.ece.unm.edu/~etanner/MPI.html I think the above error is because of the PME calculations and changing the grid spacing might work. But I dont know how to change the grid spacing. Do you have any idea regarding that? Or if you think the error is due to some other reason let me know. I am attaching the .mdp file with this email. Thanks for the help. Regards Shivkumar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php CB_20Bulk.o72899 Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fftw vs cmkl
Dallas B. Warren wrote: Thanks Mark. My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps fftw 3.2.1 - 20,027 seconds Intel cmkl - 19,792 seconds So about 1.2% faster. IIRC icc does a better job on mkl than gcc. Of course you need to make sure the PME job is being dominated by the FFT part to be sure you're measuring a relevant speed difference. The output at the end of the log file reveals this. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Msd of molecule center of mass (g_msd -mol with -rmcomm)
Hello, Does anyone have additional details about how the calculations are done for the -mol flag of g_msd when using -rmcomm? I am comparing results with and without the -mol flag. I presume that when -mol is used the file specified by the -o flag contains the average msd of the centers of mass of the molecules chosen with the index group and when -mol is not used, -o contains the average msd of atoms in the selected group. I have two specific questions: (1) Why would the msd of the COM of molecules be greater than the msd of the atoms at low dt (or at all length scales in some cases)? This does not happen when -rmcomm is not used but then the diffusion is wrong (too fast). (2) Why does the -mol msd curve up along a vertical asymtote at tmax when using -rmcomm? My system is a mixture of lipids in a bilayer run for 200 ns where COM of only the system was removed by mdrun. Trjconv was used to extract one leaflet of all lipids without water into an XTC file (e.g. upperleaflet-nojump.xtc). On this extracted sub-system, g_msd was run with -rmcomm and -lateral z while selecting for one lipid type with an index file. This was tried with and without -mol and comparing the outputs led to the questions above. Thanks, Matt --- Matthew I. Hoopes, Ph.D. Candidate Biophysics Graduate Group Department of Chemical Engineering and Material Science University of California, Davis 3118 Bainer Hall 1 Shields Ave. Davis, CA 95616 mihoo...@ucdavis.edu 530-752-6452 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpispawn.c:303 Unexpected exit status
shivkumar bale wrote: Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching the error message with this email. Have a look at it. If you need any more information let me know. Have a look at the .log file produced by mdrun, if there is one. Otherwise, this really sounds more like a job for your sysadmin, since there is no Gromacs-related output that you have shown thus far to indicate that this is a Gromacs problem. -Justin Thanks for your help. Regards Shivkumar On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: You haven't addressed any of the comments or questions I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html When asking for free help, demonstrate that you're willing to take the advice you're given, and if that fails, state what problems remain. Otherwise, it seems like you're ignoring viable suggestions. For the sake of being explicit: your .mdp file is wrong, and the dynamics are likely spurious. Solve these issues (which I have described for you!) before moving to a more peripherally-related solution. Also check the .log file; as I said before, Gromacs rarely exits without offering its own error messages about what's going wrong. There is nothing in this output that immediately suggests your PME spacing is remotely at fault, but other parameters in your .mdp file are clearly wrong. -Justin shivkumar bale wrote: Hi Gromacs Users, The error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Following is the link which might help: http://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/%7Eetanner/MPI.html http://www.ece.unm.edu/~etanner/MPI.html I think the above error is because of the PME calculations and changing the grid spacing might work. But I dont know how to change the grid spacing. Do you have any idea regarding that? Or if you think the error is due to some other reason let me know. I am attaching the .mdp file with this email. Thanks for the help. Regards Shivkumar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpispawn.c:303 Unexpected exit status
Hi Justin, Thanks for replying. No .log file is produced. Can you elaborate what do you mean by ' this really sounds more like a job for your sysadmin '. What should I exactly do to rectify this error? I am new to super computers and gromacs. Regards Shivkumar On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivkumar bale wrote: Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching the error message with this email. Have a look at it. If you need any more information let me know. Have a look at the .log file produced by mdrun, if there is one. Otherwise, this really sounds more like a job for your sysadmin, since there is no Gromacs-related output that you have shown thus far to indicate that this is a Gromacs problem. -Justin Thanks for your help. Regards Shivkumar On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: You haven't addressed any of the comments or questions I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html When asking for free help, demonstrate that you're willing to take the advice you're given, and if that fails, state what problems remain. Otherwise, it seems like you're ignoring viable suggestions. For the sake of being explicit: your .mdp file is wrong, and the dynamics are likely spurious. Solve these issues (which I have described for you!) before moving to a more peripherally-related solution. Also check the .log file; as I said before, Gromacs rarely exits without offering its own error messages about what's going wrong. There is nothing in this output that immediately suggests your PME spacing is remotely at fault, but other parameters in your .mdp file are clearly wrong. -Justin shivkumar bale wrote: Hi Gromacs Users, The error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Following is the link which might help: http://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/%7Eetanner/MPI.htmlhttp://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/~etanner/MPI.html I think the above error is because of the PME calculations and changing the grid spacing might work. But I dont know how to change the grid spacing. Do you have any idea regarding that? Or if you think the error is due to some other reason let me know. I am attaching the .mdp file with this email. Thanks for the help. Regards Shivkumar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpispawn.c:303 Unexpected exit status
shivkumar bale wrote: Hi Justin, Thanks for replying. No .log file is produced. Can you elaborate what do you mean by ' this really sounds more like a job for your sysadmin '. What should I exactly do to rectify this error? I am new to super computers and gromacs. If no output is produced, then there are plenty of potential problems - faulty Gromacs installation, buggy MPI implementation (they are out there!), node problems, etc. Whoever is in charge of the cluster (your system administrator) may be able to probe system log files or run debug analysis to see what's wrong. There's nothing more anyone here can likely provide. -Justin Regards Shivkumar On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shivkumar bale wrote: Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching the error message with this email. Have a look at it. If you need any more information let me know. Have a look at the .log file produced by mdrun, if there is one. Otherwise, this really sounds more like a job for your sysadmin, since there is no Gromacs-related output that you have shown thus far to indicate that this is a Gromacs problem. -Justin Thanks for your help. Regards Shivkumar On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: You haven't addressed any of the comments or questions I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html When asking for free help, demonstrate that you're willing to take the advice you're given, and if that fails, state what problems remain. Otherwise, it seems like you're ignoring viable suggestions. For the sake of being explicit: your .mdp file is wrong, and the dynamics are likely spurious. Solve these issues (which I have described for you!) before moving to a more peripherally-related solution. Also check the .log file; as I said before, Gromacs rarely exits without offering its own error messages about what's going wrong. There is nothing in this output that immediately suggests your PME spacing is remotely at fault, but other parameters in your .mdp file are clearly wrong. -Justin shivkumar bale wrote: Hi Gromacs Users, The error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Following is the link which might help: http://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/%7Eetanner/MPI.html http://www.ece.unm.edu/~etanner/MPI.html http://www.ece.unm.edu/~etanner/MPI.html I think the above error is because of the PME calculations and changing the grid spacing might work. But I dont know how to change the grid spacing. Do you have any idea regarding that? Or if you think the error is due to some other reason let me know. I am attaching the .mdp file with this email. Thanks for the help. Regards Shivkumar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read
RE: [gmx-users] fftw vs cmkl
3D-FFT under both situations is 21.4% and PME mesh down as 54% (figures taken from the second last and last tables in the .log file, respectively). Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 12/11/2009 11:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fftw vs cmkl Dallas B. Warren wrote: Thanks Mark. My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps fftw 3.2.1 - 20,027 seconds Intel cmkl - 19,792 seconds So about 1.2% faster. IIRC icc does a better job on mkl than gcc. Of course you need to make sure the PME job is being dominated by the FFT part to be sure you're measuring a relevant speed difference. The output at the end of the log file reveals this. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting a trajectory
Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the trajectory file. Thanks for your help Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] splitting a trajectory
Ramachandran G wrote: Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the trajectory file. Thanks for your help Make use of the -b and -e flags, which should be present in all of the analysis tools. -Justin Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] splitting a trajectory
Another option is to create a new trajectory file to use in your analysis, using trjconv Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 12/11/2009 3:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] splitting a trajectory Ramachandran G wrote: Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the trajectory file. Thanks for your help Make use of the -b and -e flags, which should be present in all of the analysis tools. -Justin Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] splitting a trajectory
Thanks for your help. I have tried the command trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro but nothing was written on output file(test.gro) and got the message WARNING no output, trajectory ended at 500 Am i doing it right? On Thu, Dec 10, 2009 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the trajectory file. Thanks for your help Make use of the -b and -e flags, which should be present in all of the analysis tools. -Justin Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] splitting a trajectory
Ramachandran G wrote: Thanks for your help. I have tried the command trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro but nothing was written on output file(test.gro) and got the message WARNING no output, trajectory ended at 500 Am i doing it right? Obviously not. If your trajectory ended at 500 ps, then frames at 87001 and 99000 ps clearly don't exist. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
