[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Hi Justin, I have another doubt on the strong posres that was included in the topology file. When do we need to remove that position restraint? Does it really affect at point of time the system? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Water molecules cannot be settled, why?
Date: Wed, 11 Jul 2012 10:32:35 +0200 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Re: Water molecules cannot be settled, why? To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=UTF-8 > Hi John, Check where the unsettling water molecule is placed. > If it's in the protein. that may be the cause of the problem. > Otherwise, it's some of the other stuff you're doing, but rule > out the simple things first. > Cheers, Tsjerk Thank you Tsjerk, I am proceeding with your recommendation. I looked at two different simulations which crashed. The unsettled water molecules appear to be far from the protein in all cases. As the details of the protocol in the last message that I posted showed, I'm using five CPU cores for my simulations. So the domain decomposition in mdrun is 5 x 1 x 1. When the simulations crash, the error handling routine outputs only the domain which contains the unsettled water molecule. In the first simulation that I examined, the domain was all solvent. No protein atoms were present. The crash occurred on step 81,240 of my final molecular dynamics run, and the atom that was identified as a problem was number 45191. So I looked at the two PDB files that were dumped, and searched for atom 45191. I think that the first file describes the system immediately before the crash, and the second file shows the results of the bad calculations, am I correct? Here is a selected portion of each file, showing atom 45191 and its neighbors: step81240b_n4.pdb ATOM 41009 OW SOL 1 74.590 46.654 65.507 ATOM 41010 HW1 SOL 1 74.580 47.272 66.294 ATOM 41011 HW2 SOL 1 73.700 46.205 65.425 ATOM 43679 OW SOL 1 71.579 49.011 70.894 ATOM 43680 HW1 SOL 1 71.730 49.197 69.924 ATOM 43681 HW2 SOL 1 71.013 49.735 71.288 ATOM 45191 OW SOL 1 72.656 46.524 71.131 ATOM 45192 HW1 SOL 1 72.614 45.938 70.322 ATOM 45193 HW2 SOL 1 72.389 47.455 70.883 ATOM 6926 OW SOL 1 75.926 46.701 73.317 ATOM 6927 HW1 SOL 1 75.024 46.674 72.886 ATOM 6928 HW2 SOL 1 76.564 47.194 72.724 ATOM 16016 OW SOL 1 73.244 51.473 72.961 ATOM 16017 HW1 SOL 1 73.712 51.310 72.092 ATOM 16018 HW2 SOL 1 73.472 52.387 73.296 step81240c_n4.pdb ATOM 41009 OW SOL 1 74.582 46.669 65.502 ATOM 41010 HW1 SOL 1 74.582 47.320 66.260 ATOM 41011 HW2 SOL 1 73.689 46.221 65.445 ATOM 43679 OW SOL 1-66321836.00084864872.00046148104.000 ATOM 43680 HW1 SOL 1 71.706 49.216 69.937 ATOM 43681 HW2 SOL 1 1085546624.000-1490344960.000-271069120.000 ATOM 45191 OW SOL 1-176865.797532401.250-1222093.250 ATOM 45192 HW1 SOL 119264928.000-53927836.000125858544.000 ATOM 45193 HW2 SOL 1 72.351 47.488 70.877 ATOM 6926 OW SOL 1 75.925 46.703 73.302 ATOM 6927 HW1 SOL 1 75.021 46.680 72.875 ATOM 6928 HW2 SOL 1 76.562 47.196 72.710 ATOM 16016 OW SOL 1 73.240 51.478 72.957 ATOM 16017 HW1 SOL 1 73.728 51.296 72.103 ATOM 16018 HW2 SOL 1 73.442 52.407 73.266 WOW. Something went seriously wrong with four atoms in that step. Are those even coordinates? For some reason, atom 45191 was selected as the one to trigger the crash report. I looked through the whole PDB file for other problems, and I found one more oxygen atom in another water molecule which had similarly wild coordinates. It was half-way across the domain, not even a neighbor of atom 45191. I had a look at atom 45191 in PyMol, and there was nothing obviously wrong with its position right before the crash. Stereo image here: http://www.flickr.com/photos/15579975@N00/7553843726/ In the second crashed simulation, only a single abnormal atom was found in the PDB file. The domain containing that water molecule did contain a part of the protein, but the water molecule was nowhere near the protein. Here's an image of that domain (unsettled water molecule marked with an amber sphere): http://www.flickr.com/photos/15579975@N00/7554770182/ I hope that helps to narrow down the problem. Thanks again. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Some interactions seem to be assigned multiple times
Dear gmx users, My system is composed of a protein and water. I am working with CHARMM36 and the current version of Gromacs, 4.5.5. For NVT equilibration , I get this error: "Software inconsistency error: Some interactions seem to be assigned multiple times" Through the mailing list, I just found that some bugs might be the reason of the error, and the Gromacs version should be current. But as I said I use the current version of Gromacs. I really don't have any idea for solving this problem. Any suggestions would be appreciated. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Final state not reached in pulling simulation
On 7/13/12 2:32 AM, Neeru Sharma wrote: Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using "position" geometry too with pull_vec1. Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? I don't know why this is happening. That's why you need to try more things to see if you can root out the issue. There are a whole host of factors that can act against the pulling force. You're not using any sort of position restraints, are you? The other thing to keep in mind is that if your initial distance is 0.7 nm, and you pull for 10 ns at 0.05 nm/ns, you should in theory end up with a distance of 0.2 nm, not 0.3 nm. That is, assuming that the pulled group is free to move and thus smoothly goes along with the spring. Other forces within the structure may act in opposition. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 1:44 AM, J Peterson wrote: Thanks for the comment. By the way how to make a bigger box at this time of the tutorial without affecting any part of the system. Can I use editconf with slightly bigger number for z-axis (something like 6.7 which was 5.7 before)? The box should be sufficiently large so as to avoid spurious interactions across periodic boundaries. The size is thus motivated by the length of the cutoffs used. Increasing the box by 1.0 nm might be just enough, but you should calculate this very carefully. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 4:14 AM, J Peterson wrote: Hi Justin, I have another doubt on the strong posres that was included in the topology file. When do we need to remove that position restraint? Does it really affect at point of time the system? The strong restraints are only needed for InflateGRO. During equilibration, position restraints with a normal magnitude are appropriate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Melting simulations - regd
On 7/13/12 2:27 AM, sukumar rapolu wrote: Hello gmx users, I am doing melting simulations of a polymer in gromacs, for this am giving output from a production run of particular temperature as the input for equilibration at next temperature and generating velocities in equilibration at each temperature by using gen_vel = yes. Here my doubt is, as I am using output from production as input for equilibration so do I have to use continuation= yes in my equilibration mdp file or as I am generating velocities at each temperature during equilibration do I have to use continuation= no ? If you're using the structure from a previous run that used constraints, the difference between these two settings should be minimal. But since you're basically starting totally new simulations, you can't go wrong with "continuation = no." -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Thanks Justin, The explanations are very very useful during my course of simulating a protein with POPC. I also would like to get explanation on how to simulate a protein which has only its N-terminal region embedded in the membrane but the rest in solvent. What is the easy and accurate way to do it? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 6:44 AM, J Peterson wrote: Thanks Justin, The explanations are very very useful during my course of simulating a protein with POPC. I also would like to get explanation on how to simulate a protein which has only its N-terminal region embedded in the membrane but the rest in solvent. What is the easy and accurate way to do it? Position the protein with editconf -center and follow all the other steps in the same way. The dimensions of the box become quite important in such a case. There are some general tips on such placement in another of my tutorials: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] NVT with shape fluctuations
Hi, I would like to know if it's possible to perform an NVT simulation but letting the box shape to fluctuate. Thank you -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-with-shape-fluctuations-tp4999411.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Any ways to read/convert .g96 file format and keep the precision?
Reading trajectories in .g96 format is broken. Please use a different file format. -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: Karjaan lukio --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Any ways to read/convert .g96 file format and keep the precision?
Sorry about double posting, I have some problems with my laptop... Question: Are there any ways to read/convert positions in .g96 file format and keep the precision (%15.9f) for a structure to be read by mdrun -rerun myfile.g96 ? I get an annoying error message: >Reading trajectories in .g96 format is broken. Please use a different file >format. with mdrun and trjconv Terveisin Markus On 13/07/2012, Markus Kaukonen wrote: > Reading trajectories in .g96 format is broken. Please use a different > file format. > > > -- > --www=http://www.iki.fi/markus.kaukonen > --markus.kauko...@iki.fi > --office: Karjaan lukio > --home: Viinirinne 3 F 12, 02630 Espoo, FIN > --tel: h 045-1242068 > -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: Karjaan lukio --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Final state not reached in pulling simulation
Thanks Justin for all your comments and suggestion. I am not using any position restraints as of now. But I will try out more parameters and more options. Thanks again. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999414.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mdrun graceful exit
On Fri, Jul 6, 2012 at 1:13 AM, Mark Abraham wrote: > > Possibly not. This might be another instance of the GROMACS team having not > put much effort into the EM code on the theory that it doesn't run for long > enough, so have enough time for developer effort to pay off in significantly > better user experience, given most people's workflows. > Thanks, Mark. Probably I'll add a feature request in redmine then, since I have no idea how to code such signal handling. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_saltbr speed
Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. Thank you With Regards Kavya On Thu, Jul 12, 2012 at 6:11 PM, Kavyashree M wrote: > Dear Sir, > > Thank you It worked :). a very usefull suggestion. > But it did not promt to choose any option. I used > index file. > > Thank you > Kavya > > On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul wrote: >> >> >> On 7/12/12 8:31 AM, Kavyashree M wrote: >>> >>> Ok may be i need to specify an index file. I will try that. >>> And regarding the WARNING: this .tpx file is not fully functional. >>> I hope it will work fine enough to finish g_saltbr calculation? >>> >> >> In principle, you should be prompted to choose a default group, but you can >> also use a custom index group as needed. >> >> The warning message is intended to note that the .tpr file you produce will >> not likely work for running an actual simulation. It should be fine for >> analysis. >> >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> 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 >> * Only plain text messages are allowed! >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_saltbr speed
On 7/13/12 11:50 AM, Kavyashree M wrote: Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. How long is the trajectory? How many frames? What is the size of the file on disk? It sounds to me like you're simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_saltbr speed
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. Thank you kavya On Fri, Jul 13, 2012 at 9:22 PM, Justin A. Lemkul wrote: > > > On 7/13/12 11:50 AM, Kavyashree M wrote: >> >> Dear users, >> >> Its the continuation of the question I asked yesterday, Inorder to reduce >> the memory usage during g_saltbr calculations i got the trajectory of only >> protein, and tpr file without water and was able to successfully run it. >> But >> unfortunately this again got stopped at 36ns as it had stopped when i was >> using the whole trajectory. I tried with -dt 2, still the same problem >> exists. >> Kindly suggest a way out of this situation. >> > > How long is the trajectory? How many frames? What is the size of the file > on disk? It sounds to me like you're simply exhausting available memory, so > the only advice is in the link I posted before - use fewer frames or use a > machine that has more memory to do the analysis. > > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_saltbr speed
On 7/13/12 12:05 PM, Kavyashree M wrote: Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. I can't see a reason why the file itself would present a problem. I have run g_saltbr on similarly sized systems. Sorry, I can't offer an explanation as to why it's stopping prematurely. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_saltbr speed
Ok... I will try other options. Thanks Kavya On Fri, Jul 13, 2012 at 10:23 PM, Justin A. Lemkul wrote: > > > On 7/13/12 12:05 PM, Kavyashree M wrote: >> >> Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will >> that be insufficient? I have previously run other analysis which used to >> take >> huge memory, for eg. covariance analysis, in a system with much lesser >> memory >> even though CPU usage was low the job used to finish. But in this case its >> not >> so. >> > > I can't see a reason why the file itself would present a problem. I have > run g_saltbr on similarly sized systems. Sorry, I can't offer an > explanation as to why it's stopping prematurely. > > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Melting simulations - regd
Dear Justin, Thank you for your reply, here I have one more doubt, I am using 'pcoupltype= anisotropic' in my simulationa as the polymers are aniostropic, I have searched for compressibility values of system but i couldn't find is there any generalized way to set up compressibility values. Thank you, -- View this message in context: http://gromacs.5086.n6.nabble.com/Melting-simulations-regd-tp4999398p4999421.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
