[gmx-users] Obtain frames from every one ps
Dear All, I need help in obtaining frames from every one ps of a trajectory. My problem is as described: I obtained a 100ns trajectory, I get one frame for every 5 ps from my initial, but my new trajectory is generated by catenating different frames that fall in the bins of PCA space of the first two PC components with lowest energy. Now that, I want to do the analysis like angle average, RMSD etc on all the frames, I would like to know how to obtain frames from this new trajectory at every one ps. Please help me. Thanks in advance. Dr. Asha Latha Sreshty, Post Doctoral Fellow, Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560012 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] doubt in remd
Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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: RDF output has no data
So there is a problem with your trajectory file. Try to understand what kind of problem it is. I can recollect that I experienced something like that why translating CPMD trajectory to GROMACS. Maybe, it does not write time for each frame at the right place -- just a guess. Dr. Vitaly Chaban On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy venkat...@gmail.com wrote: Sir I tried g_msd, after asking for group selection the program appears not to read the frames as it remains stuck at reading frame 0, time 0.00. What to do? Thanks On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Do you experience this problem with g_rdf only, or with all gromacs analysis utilities? On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote: Sir I loaded the trajectory. There doesn't seem to be anything wrong with it. Have no clue whats going wrong Thanks On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I believe the problem is in the way which you used to convert AMBER trajectory to the GROMACS trajectory I would suggest to try gmxdump and see what your trajectory looks like. Oe maybe even better - try to visualize it in VMD to see if the format is correct. Dr. Vitaly Chaban Sir I was using an old version. Now I used 4.5.5, it still gives me the same blank output file. Kindly suggest how to go about solving this Thanks On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com wrote: There was no fatal error preceding the output. After selecting the groups following are the output on the screen Reading frame 1 time0.100 Warning: can not make broken molecules whole without a run input file, don't worry, mdrun doesn't write broken molecules This message is from a prehistoric version of g_rdf. Please get a new one. Mark Reading frame2000 time 200.000 gcq#69: The Wheels On the Bus Go Round and Round (J. Richman) And the rdf.xvg file looks like this #This file was created Sat Apr 6 10:54:13 2013 # by the following command: # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg # # g_rdf is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title Radial Distribution @xaxis label r @yaxis label @TYPE xy @ subtitle O21-H2__CAT 0.001 1 ~ Whats going wrong? Please help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] doubt in remd
Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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] how to split the disulfide bonds in CYSH?
Dear, In my system ,there are many disulfide bonds in my protein. i want to split these disulfide bonds to CYSH. I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top -water spce -ss ,but i get the CYS2. please help me ,thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] doubt in remd
The gromacs web page links to this server for REMD temperature generation: http://folding.bmc.uu.se/remd/ On 9 Apr 2013, at 08:34, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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] doubt in remd
Hi! I'm also working on REMD in these days. For temperature spacing you can use this web site: http://folding.bmc.uu.se/remd/ In order to find the most probable structure, which should be the global minimum, I think you can work with cluster analysis based on rmsd. Or it can be also useful a secondary structure analysis along the trajectory (if it is interesting for your system). If anyone else have some ideas I'm also looking for them. Simone 2013/4/9 Nikunj Maheshwari nixcrazyfor...@gmail.com Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
Dear Dr. Vitaly Chaban, Thanks very much for your patient and detailed suggestions on this problem. Actually, I am doing what your suggested now. I optimized the copper-ligand complex using QM method, and then did some QM scannings to derive the bond and angle force constants. Right now, I am doing the MM scanning using the same coordinates which were used in the QM scanning. What we want is that the MM curves can reproduce the QM curves. But some of them agreed well, some of them did not. So I try to tune the sigma of the liganded atoms, however, it is a little complicated to tune many liganded atoms at the same time. I am still trying to work it out. It seems that you have much experience on such problems, could you please give me some suggestions on tuning the sigmas of atoms again? Thanks very much in advance! All the best, Qinghua Liao On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote: On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com mailto:fantastic...@gmail.com wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient explanation. Yeah, you are right, that is what I want to know: how you tuned this parameter? Since then, if I want to set a new atom type and I know its vdw radius, so how should I set the sigma for it based on the vdw radius, You cannot set the sigma based ONLY on the VDW radius. which should be in agreement with OPLS-AA/L force filed? Could you give me some suggestions? I guess that I have to tune it by myself this time, right? Thanks in advance! I would do the following: 1) Optimize ion-ligand complex using ab initio. Write down binding energy and optimal distance; 2) Construct topology for classical MD using approximate sigma; 3) Calculate energy and distance from classical MD; 4) Compare them to distance and energy from ab initio; 5) If you are not satisfied, adjust your sigma; 6) Repeat classical MD until the difference between ion-ligand distance in classical MD becomes reasonably similar to that in ab initio. To preserve compatibility with OPLS, use the same level of theory in ab initio, which they used when derived OPLS. Keep in mind that their original level of theory is not so perfect... Dr. Vitaly Chaban All the best, Qinghua Liao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Maximum protein size for REMD?
Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Maximum protein size for REMD?
I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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] amber99 with berger's lipids
By the way during simulation of the membrane-protein systems in the Amber99sb ff (with berger lipids) I've noticed decreased of my system in the Z-direction ( I've observed the same also during simulation of such systems in the Charm full atomic ff). In both cases the observed effect was seen in both GPU and non-gpu regimes with different cutoffs. It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff with berger lipids) I didnt observe such decreasing in the Z - dimension of my bilayer. The only difference was in the water models (spc in the gromos and tip3p in the amber or charm). Might it be relevant ? Should I switch to the spc water with the amber ? James 2013/4/8 Justin Lemkul jalem...@vt.edu On Mon, Apr 8, 2013 at 7:50 AM, James Starlight jmsstarli...@gmail.com wrote: In literature I found that the ussage of 1.0 cutoffs should give good results but in the antechamber manual I've seen that usages of 1.2 cutoofs ( with GAFF) should be used. So what cut-offs should I use for protein-ligand complexes done in amber ? (assuming that I simulate my system in the berger lipids ) Do a few test runs and see. I would think the cutoff value would more strongly affect the lipids, not the ligand, whose interactions are comparatively few and relatively local. If you use the Verlet cutoff scheme in version 4.6, it's largely irrelevant since there will not be any missed interactions either way. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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] Maximum protein size for REMD?
How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient and detailed suggestions on this problem. Actually, I am doing what your suggested now. I optimized the copper-ligand complex using QM method, and then did some QM scannings to derive the bond and angle force constants. Right now, I am doing the MM scanning using the same coordinates which were used in the QM scanning. What we want is that the MM curves can reproduce the QM curves. I think it is simply impossible in your case to reproduce the QM curves. You neglect charge transfer from copper to the ligand, resulting a chemical bond formation, you neglect finite T effect in your MD. If you want to remain in the framework of LJ+Coulomb, the best think you can get is reproduction of ion-ligand binding energy and more or less adequate distance ion-closest atom of the ligand But some of them agreed well, some of them did not. So I try to tune the sigma of the liganded atoms, however, it is a little complicated to tune many liganded atoms at the same time. I am still trying to work it out. Start from the sigma for ion-closest atom of the ligand. All other atoms will adjust automatically, since they are connected all together within the ligand. My personal viewpoint, which you may share or not, is not to do anything with sigmas of other atoms of the ligand. It is best for future portability to limit refinement to the ion only. It seems that you have much experience on such problems, could you please give me some suggestions on tuning the sigmas of atoms again? Thanks very much in advance! All the best, Qinghua Liao On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote: On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.comwrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient explanation. Yeah, you are right, that is what I want to know: how you tuned this parameter? Since then, if I want to set a new atom type and I know its vdw radius, so how should I set the sigma for it based on the vdw radius, You cannot set the sigma based ONLY on the VDW radius. which should be in agreement with OPLS-AA/L force filed? Could you give me some suggestions? I guess that I have to tune it by myself this time, right? Thanks in advance! I would do the following: 1) Optimize ion-ligand complex using ab initio. Write down binding energy and optimal distance; 2) Construct topology for classical MD using approximate sigma; 3) Calculate energy and distance from classical MD; 4) Compare them to distance and energy from ab initio; 5) If you are not satisfied, adjust your sigma; 6) Repeat classical MD until the difference between ion-ligand distance in classical MD becomes reasonably similar to that in ab initio. To preserve compatibility with OPLS, use the same level of theory in ab initio, which they used when derived OPLS. Keep in mind that their original level of theory is not so perfect... Dr. Vitaly Chaban All the best, Qinghua Liao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Maximum protein size for REMD?
I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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 * 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] Maximum protein size for REMD?
Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started using polynomial fit of the average energies we obtained from our first run. Do you have any thoughts on that? On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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 * 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 * 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: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
Dear Dr. Vitaly Chaban, Thanks very much again. I am sorry for the unclear, charge transfer was also taken into account for the complex, I did not mentioned in the last e-mail. What do you mean by finite T effect in MD? Kinetics? For the reproduction of binding energy, I guess I know how to do it using QM method. Simply, I just need to do three single point calculations for complex, ligands and ion, respectively. For MM method, it is similar, however, I am not sure I get get the MM energy for just one ion. Is my understanding right? Thanks for all your explanations and suggestions on this problems! All the best, Qinghua Liao On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote: On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com mailto:fantastic...@gmail.com wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient and detailed suggestions on this problem. Actually, I am doing what your suggested now. I optimized the copper-ligand complex using QM method, and then did some QM scannings to derive the bond and angle force constants. Right now, I am doing the MM scanning using the same coordinates which were used in the QM scanning. What we want is that the MM curves can reproduce the QM curves. I think it is simply impossible in your case to reproduce the QM curves. You neglect charge transfer from copper to the ligand, resulting a chemical bond formation, you neglect finite T effect in your MD. If you want to remain in the framework of LJ+Coulomb, the best think you can get is reproduction of ion-ligand binding energy and more or less adequate distance ion-closest atom of the ligand But some of them agreed well, some of them did not. So I try to tune the sigma of the liganded atoms, however, it is a little complicated to tune many liganded atoms at the same time. I am still trying to work it out. Start from the sigma for ion-closest atom of the ligand. All other atoms will adjust automatically, since they are connected all together within the ligand. My personal viewpoint, which you may share or not, is not to do anything with sigmas of other atoms of the ligand. It is best for future portability to limit refinement to the ion only. It seems that you have much experience on such problems, could you please give me some suggestions on tuning the sigmas of atoms again? Thanks very much in advance! All the best, Qinghua Liao On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote: On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com mailto:fantastic...@gmail.com wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient explanation. Yeah, you are right, that is what I want to know: how you tuned this parameter? Since then, if I want to set a new atom type and I know its vdw radius, so how should I set the sigma for it based on the vdw radius, You cannot set the sigma based ONLY on the VDW radius. which should be in agreement with OPLS-AA/L force filed? Could you give me some suggestions? I guess that I have to tune it by myself this time, right? Thanks in advance! I would do the following: 1) Optimize ion-ligand complex using ab initio. Write down binding energy and optimal distance; 2) Construct topology for classical MD using approximate sigma; 3) Calculate energy and distance from classical MD; 4) Compare them to distance and energy from ab initio; 5) If you are not satisfied, adjust your sigma; 6) Repeat classical MD until the difference between ion-ligand distance in classical MD becomes reasonably similar to that in ab initio. To preserve compatibility with OPLS, use the same level of theory in ab initio, which they used when derived OPLS. Keep in mind that their original level of theory is not so perfect... Dr. Vitaly Chaban All the best, Qinghua Liao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] reading Hydrogens from an itp file
Dear All, I have a pdb file in which has only heavy atoms (means all atoms except hydrogen) and a corresponding itp file with all atoms (including hydrogens). The heavy atoms in pdb file are in sequence order as in itp file. e.g. itp pdb (no Hydrogens) * C1 C1 H1 C2 H2 O1 H3 C2 H4 H5 O1 With this pdb (missing Hs ) Is there any way to add hydrogens (which are in itp file) to write a *.gro file having all heavy and hydrogen atoms? regards, Vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Lipid membrane partially broken and create huge voids after NVT
Gromacs users, My complex heterogenous system has DPPC+ Protein+ligand. I have packed lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 got after 24th iteration) followed by adding solvent and neutralize the system by adding CL35 NA 39, since my system has -3.999 non zero total charge. Then the minimized system has the energy -2.8989 with Max force= 9.58 converged normally in step 464 step. I used lipid constraints in the file DPOSRES_LIPID.itp before NVT ; position restraint file for DPPC P8 [ position_restraints ] ; i funct fcxfcyfcz 81 0 0 1000 --- My topology has the last part... --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include lig topology #include lig.itp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include DSTRONG_POSRES_B.itp #endif ; Include DPPC topology #include dppc.itp ;strong position restraints for DPPC #ifdef POSRES_LIPID #include DPOSRES_LIPID.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name complex protein in water [ molecules ] ; Compound#mols Protein_G 1 Lig 1 DPPC 125 SOL 3199 CL 35 NA 39 --- There is no grompp error and no problem till NVT, after this equillibration, half of the DPPC along with SOL is no showing in VMD. Could any suggestions on this behavior. Thanks in advance -Shine -- View this message in context: http://gromacs.5086.x6.nabble.com/Lipid-membrane-partially-broken-and-create-huge-voids-after-NVT-tp5007128.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 * 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] how to extract last frame?
Hello: I am trying to extract last frame of my MD simulations with command: trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb but it said: WARNING no output, last frame read at t=751.4 gcq#286: Oh, There Goes Gravity (Eminem) thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] how to extract last frame?
http://gromacs.5086.x6.nabble.com/How-to-get-the-number-of-frames-contained-by-an-xtc-trajectory-file-td4998050.html Cheers, Tsjerk On Tue, Apr 9, 2013 at 11:37 AM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to extract last frame of my MD simulations with command: trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb but it said: WARNING no output, last frame read at t=751.4 gcq#286: Oh, There Goes Gravity (Eminem) thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl fantastic...@gmail.comwrote: Dear Dr. Vitaly Chaban, Thanks very much again. I am sorry for the unclear, charge transfer was also taken into account for the complex, I did not mentioned in the last e-mail. What do you mean by finite T effect in MD? Kinetics? I mean thermal motion. You have an optimal structure/energy at 0K in QM. In MD you want to simulate at higher T, I guess. The optimal structures in both cases may be very similar, but may be not so similar. I am just saying that you should not expect ideal coincidence of energy vs. distance curves. For the reproduction of binding energy, I guess I know how to do it using QM method. Simply, I just need to do three single point calculations for complex, ligands and ion, respectively. And correct for BSSE. For MM method, it is similar, however, I am not sure I get get the MM energy for just one ion. This energy is zero within classical MD, since you do not consider electrons and nucleus, as you do in QM. Only one calculation is needed for MM. You define the charge groups, such as ion and ligand and look at the interaction between them (g_energy). Is my understanding right? Thanks for all your explanations and suggestions on this problems! All the best, Qinghua Liao On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote: On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.comwrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient and detailed suggestions on this problem. Actually, I am doing what your suggested now. I optimized the copper-ligand complex using QM method, and then did some QM scannings to derive the bond and angle force constants. Right now, I am doing the MM scanning using the same coordinates which were used in the QM scanning. What we want is that the MM curves can reproduce the QM curves. I think it is simply impossible in your case to reproduce the QM curves. You neglect charge transfer from copper to the ligand, resulting a chemical bond formation, you neglect finite T effect in your MD. If you want to remain in the framework of LJ+Coulomb, the best think you can get is reproduction of ion-ligand binding energy and more or less adequate distance ion-closest atom of the ligand But some of them agreed well, some of them did not. So I try to tune the sigma of the liganded atoms, however, it is a little complicated to tune many liganded atoms at the same time. I am still trying to work it out. Start from the sigma for ion-closest atom of the ligand. All other atoms will adjust automatically, since they are connected all together within the ligand. My personal viewpoint, which you may share or not, is not to do anything with sigmas of other atoms of the ligand. It is best for future portability to limit refinement to the ion only. It seems that you have much experience on such problems, could you please give me some suggestions on tuning the sigmas of atoms again? Thanks very much in advance! All the best, Qinghua Liao On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote: On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.comwrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient explanation. Yeah, you are right, that is what I want to know: how you tuned this parameter? Since then, if I want to set a new atom type and I know its vdw radius, so how should I set the sigma for it based on the vdw radius, You cannot set the sigma based ONLY on the VDW radius. which should be in agreement with OPLS-AA/L force filed? Could you give me some suggestions? I guess that I have to tune it by myself this time, right? Thanks in advance! I would do the following: 1) Optimize ion-ligand complex using ab initio. Write down binding energy and optimal distance; 2) Construct topology for classical MD using approximate sigma; 3) Calculate energy and distance from classical MD; 4) Compare them to distance and energy from ab initio; 5) If you are not satisfied, adjust your sigma; 6) Repeat classical MD until the difference between ion-ligand distance in classical MD becomes reasonably similar to that in ab initio. To preserve compatibility with OPLS, use the same level of theory in ab initio, which they used when derived OPLS. Keep in mind that their original level of theory is not so perfect... Dr. Vitaly Chaban All the best, Qinghua Liao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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: Lipid membrane partially broken and create huge voids
My complex heterogenous system has DPPC+ Protein+ligand. I have packed lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 got after 24th iteration) followed by adding solvent and neutralize the system by adding CL35 NA 39, since my system has -3.999 non zero total charge. Then the minimized system has the energy -2.8989 with Max force= 9.58 converged normally in step 464 step. I used lipid constraints in the file DPOSRES_LIPID.itp before NVT There is no grompp error and no problem till NVT, after this equillibration, half of the DPPC along with SOL is no showing in VMD. Could any suggestions on this behavior. I think your particles are still there... Try to adjust VMD settings. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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: Re: Re: Re: help with chromophore of a GFP
Dear gmx-users, dear Mark, I still have problems with my parametrization, and I wrote a message describing in details the problems, but it appears to be too large and it is being held on hold (see below). How can I send it to the gmx-users list? Can I write to personal emails? Please let me know how to find a way to send you all information. Thanks Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) Messaggio originale Oggetto:Your message to gmx-users awaits moderator approval Data: Tue, 09 Apr 2013 12:27:12 +0200 Mittente: gmx-users-boun...@gromacs.org A: amarabo...@unisa.it Your mail to 'gmx-users' with the subject Re: Re: help with chromophore of a GFP Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 82829 bytes with a limit of 50 KB Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://lists.gromacs.org/mailman/confirm/gmx-users/d1016c183df6d3c4e6314a1046cb51ad4175926b -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Lipid membrane partially broken and create huge voids after NVT
After NVT, usually the lipid bilayer move away from each other creating some voids, which occurs due to absence of pressure coupling. But its not a problem. You can go ahead and carry out NPT and see that bilayer has settled to normal position. -Anirban On Tue, Apr 9, 2013 at 3:04 PM, sdshine sdsh...@gmail.com wrote: Gromacs users, My complex heterogenous system has DPPC+ Protein+ligand. I have packed lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 got after 24th iteration) followed by adding solvent and neutralize the system by adding CL35 NA 39, since my system has -3.999 non zero total charge. Then the minimized system has the energy -2.8989 with Max force= 9.58 converged normally in step 464 step. I used lipid constraints in the file DPOSRES_LIPID.itp before NVT ; position restraint file for DPPC P8 [ position_restraints ] ; i funct fcxfcyfcz 81 0 0 1000 --- My topology has the last part... --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include lig topology #include lig.itp ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include DSTRONG_POSRES_B.itp #endif ; Include DPPC topology #include dppc.itp ;strong position restraints for DPPC #ifdef POSRES_LIPID #include DPOSRES_LIPID.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name complex protein in water [ molecules ] ; Compound#mols Protein_G 1 Lig 1 DPPC 125 SOL 3199 CL 35 NA 39 --- There is no grompp error and no problem till NVT, after this equillibration, half of the DPPC along with SOL is no showing in VMD. Could any suggestions on this behavior. Thanks in advance -Shine -- View this message in context: http://gromacs.5086.x6.nabble.com/Lipid-membrane-partially-broken-and-create-huge-voids-after-NVT-tp5007128.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 * 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 * 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] a gro file at the end of simulation
Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of simulation? regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] (no subject)
Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of simulation? regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] a gro file at the end of simulation
On Tue, Apr 9, 2013 at 8:02 AM, Za Pour za.p...@yahoo.com wrote: Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of simulation? From mdrun -h: The structure file (-c) contains the coordinates and velocities of the last step. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] Obtain frames from every one ps
On Tue, Apr 9, 2013 at 2:13 AM, Ashalatha Sreshty sreshty...@gmail.comwrote: Dear All, I need help in obtaining frames from every one ps of a trajectory. My problem is as described: I obtained a 100ns trajectory, I get one frame for every 5 ps from my initial, but my new trajectory is generated by catenating different frames that fall in the bins of PCA space of the first two PC components with lowest energy. Now that, I want to do the analysis like angle average, RMSD etc on all the frames, I would like to know how to obtain frames from this new trajectory at every one ps. If you're binning structures that were produced every 5 ps, there's no way to say that they occurred every 1 ps. Moreover, isn't time rather irrelevant if you've binned structures that may not be continuous in time, anyway? You can assign whatever frame interval you like with trjconv -timestep, but whether or not doing so makes any sense is up to you to decide. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] how to split the disulfide bonds in CYSH?
On Tue, Apr 9, 2013 at 3:18 AM, aixintiankong aixintiank...@126.com wrote: Dear, In my system ,there are many disulfide bonds in my protein. i want to split these disulfide bonds to CYSH. I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top -water spce -ss ,but i get the CYS2. The above command produces CYSH for me. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] reading Hydrogens from an itp file
On Tue, Apr 9, 2013 at 5:19 AM, gromacs query gromacsqu...@gmail.comwrote: Dear All, I have a pdb file in which has only heavy atoms (means all atoms except hydrogen) and a corresponding itp file with all atoms (including hydrogens). The heavy atoms in pdb file are in sequence order as in itp file. e.g. itp pdb (no Hydrogens) * C1 C1 H1 C2 H2 O1 H3 C2 H4 H5 O1 With this pdb (missing Hs ) Is there any way to add hydrogens (which are in itp file) to write a *.gro file having all heavy and hydrogen atoms? Write an .hdb entry and pdb2gmx will do it for you. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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: RDF output has no data
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: So there is a problem with your trajectory file. Try to understand what kind of problem it is. e.g. by using gmxcheck and/or gmxdump (on a small version of your data!) to see what information is present. Mark I can recollect that I experienced something like that why translating CPMD trajectory to GROMACS. Maybe, it does not write time for each frame at the right place -- just a guess. Dr. Vitaly Chaban On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy venkat...@gmail.com wrote: Sir I tried g_msd, after asking for group selection the program appears not to read the frames as it remains stuck at reading frame 0, time 0.00. What to do? Thanks On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Do you experience this problem with g_rdf only, or with all gromacs analysis utilities? On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote: Sir I loaded the trajectory. There doesn't seem to be anything wrong with it. Have no clue whats going wrong Thanks On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I believe the problem is in the way which you used to convert AMBER trajectory to the GROMACS trajectory I would suggest to try gmxdump and see what your trajectory looks like. Oe maybe even better - try to visualize it in VMD to see if the format is correct. Dr. Vitaly Chaban Sir I was using an old version. Now I used 4.5.5, it still gives me the same blank output file. Kindly suggest how to go about solving this Thanks On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com wrote: There was no fatal error preceding the output. After selecting the groups following are the output on the screen Reading frame 1 time0.100 Warning: can not make broken molecules whole without a run input file, don't worry, mdrun doesn't write broken molecules This message is from a prehistoric version of g_rdf. Please get a new one. Mark Reading frame2000 time 200.000 gcq#69: The Wheels On the Bus Go Round and Round (J. Richman) And the rdf.xvg file looks like this #This file was created Sat Apr 6 10:54:13 2013 # by the following command: # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg # # g_rdf is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title Radial Distribution @xaxis label r @yaxis label @TYPE xy @ subtitle O21-H2__CAT 0.001 1 ~ Whats going wrong? Please help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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] Maximum protein size for REMD?
On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started using polynomial fit of the average energies we obtained from our first run. Do you have any thoughts on that? You can space them however you want, but you will only get exchanges if they are close enough in temperature. The spacing returned by the generator is not small because it wants you to use excess compute resources! It needs to be small for big systems. Mark On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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 * 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 * 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 * 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 * 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: Re: Re: Re: help with chromophore of a GFP
On Tue, Apr 9, 2013 at 12:26 PM, Anna Marabotti amarabo...@unisa.it wrote: Dear gmx-users, dear Mark, I still have problems with my parametrization, and I wrote a message describing in details the problems, but it appears to be too large and it is being held on hold (see below). How can I send it to the gmx-users list? Can I write to personal emails? Please let me know how to find a way to send you all information. Discussing the contents of a file linked from and hosted on a sharing service like Google Drive or Dropbox is appropriate - or better still, discuss snippets while providing the whole context for reference. Broadcasting large files to the thousands of people subscribed to gmx-users is bad netcitizenship, so we stop people doing that. Apparently nobody reads the moderator list any more :-) Mark Thanks Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) Messaggio originale Oggetto:Your message to gmx-users awaits moderator approval Data: Tue, 09 Apr 2013 12:27:12 +0200 Mittente: gmx-users-boun...@gromacs.org A: amarabo...@unisa.it Your mail to 'gmx-users' with the subject Re: Re: help with chromophore of a GFP Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 82829 bytes with a limit of 50 KB Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://lists.gromacs.org/mailman/confirm/gmx-users/d1016c183df6d3c4e6314a1046cb51ad4175926b -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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] doubt in remd
On Tue, Apr 9, 2013 at 8:29 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? Doing a simulation is useless until you have thought about what you want to observe from it. Only then can you design the simulation so it might show what you want to observe - or go do something more profitable if it won't be possible to observe! Constructing a free energy surface from the structures in a single ensemble is straightforward (e.g. Baumketner Shea papers), and that the simulation was REMD is immaterial. 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/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 * 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] amber99 with berger's lipids
On Tue, Apr 9, 2013 at 9:59 AM, James Starlight jmsstarli...@gmail.com wrote: By the way during simulation of the membrane-protein systems in the Amber99sb ff (with berger lipids) I've noticed decreased of my system in the Z-direction ( I've observed the same also during simulation of such systems in the Charm full atomic ff). In both cases the observed effect was seen in both GPU and non-gpu regimes with different cutoffs. It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff with berger lipids) I didnt observe such decreasing in the Z - dimension of my bilayer. The only difference was in the water models (spc in the gromos and tip3p in the amber or charm). Might it be relevant ? Should I switch to the spc water with the amber ? On principle, that is a bad idea. The force fields are parametrized to work with a particular water model, and you should only use another one after careful testing that there is a suitable benefit that outweighs any drawback. They are not plug and play. You have observed two different systems show different behaviour contracting in the Z direction. Why do you think one is abnormal and one is not? 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/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] Gromacs Building Blocks
Hello I read about Gromacs building blocks ( http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks ) and there is written following table. How to do a MD Smiluation with this building blocks? Greetings Abbrev. Source 2 Full Name FAD ffgmx.rtp O flavin adenine dinucleotide -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Gromacs Building Blocks
On Tue, Apr 9, 2013 at 9:59 AM, Lara Bunte lara.bu...@yahoo.de wrote: Hello I read about Gromacs building blocks ( http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks) and there is written following table. How to do a MD Smiluation with this building blocks? A building block is just some species that Gromacs recognizes by default, e.g. it is an .rtp entry. That list is probably very outdated and likely only applies to gmx.ff, which no one should be using for anything. Consult your chosen force field's .rtp file for what it supports. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] General conceptual question about advantage of GPUs
Hi, For the past 2 years I have been running Gromacs on a standard Linux cluster (with nodes containing 24 CPUs). As you know, Gromacs scales excellently (and is super efficient), and since the CPUs are Intel Xeon 2.4 GHz processors, the simulations run quite fast (I can run 10 ns of ~7000 atoms in ~2 days on 24 CPUs). Can I expect GPUs to be any or much faster than these CPUs? There is a rumor in the department that GPUs can give a performance increase of 10-40 times relative to CPUs, although that group is using another MD package. I am curious whether this performance improvement is typical. (I would not expect it for Gromacs, though, since Gromacs is already super fast!) If you have time, do you know of any review or opinion papers that might discuss the advantages (advantages of performance or otherwise) of using GPUs over CPUs? Thanks for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] autocorrelation function of hydrogen bond : g_hbond
Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Why there is not smooth exponential plot. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] autocorrelation function of hydrogen bond : g_hbond
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] General conceptual question about advantage of GPUs
On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi, For the past 2 years I have been running Gromacs on a standard Linux cluster (with nodes containing 24 CPUs). As you know, Gromacs scales excellently (and is super efficient), and since the CPUs are Intel Xeon 2.4 GHz processors, the simulations run quite fast (I can run 10 ns of ~7000 atoms in ~2 days on 24 CPUs). Can I expect GPUs to be any or much faster than these CPUs? You can try it out yourself for free and see: http://www.nvidia.com/object/gpu-test-drive.html?cid=gputestdrive I would expect better CPU performance, honestly. Have you done benchmarking on your system to see if fewer processors actually achieve better performance by eliminating some communication overhead? Using more processors is not necessarily better. There is a rumor in the department that GPUs can give a performance increase of 10-40 times relative to CPUs, although that group is using another MD package. I am curious whether this performance improvement is typical. (I would not expect it for Gromacs, though, since Gromacs is already super fast!) Relative speedup depends heavily upon what is being compared. Gromacs has a very fast baseline, so the relative speedup may not be as high as other codes that are not as intrinsically fast on CPU :) The GPU performance of Gromacs, in absolute terms, is very impressive. We run simulations of ~150,000 atoms on a single GPU card (which is somewhat outdated) and can achieve around 10 ns/day. Newer hardware would undoubtedly perform better. If you have time, do you know of any review or opinion papers that might discuss the advantages (advantages of performance or otherwise) of using GPUs over CPUs? Hopefully very soon, Erik's webinar from last week will be posted online ( http://www.gputechconf.com/page/gtc-express-webinar.html). I learned a lot from it, and I suspect others will as well. There is plenty of literature about GPU development in MD simulations, but again, be aware of unequal comparisons and baselines. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] autocorrelation function of hydrogen bond : g_hbond
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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] GROMACS 4.6 with GPU acceleration (double presion)
Dear experts, I have the following question. I am trying to compile GROMACS 4.6.1 with GPU acceleration and have the following diagnostics: # cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCUDA_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF CMake Error at cmake/gmxManageGPU.cmake:46 (message): GPU acceleration is not available in double precision! Call Stack (most recent call first): CMakeLists.txt:143 (include) Are there any plans to have double precision with GPU acceleration in the coming version of GROMACS or this will not happen in the nearest future. Thanks and regards, Mikhail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] autocorrelation function of hydrogen bond : g_hbond
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that what you see? Erik On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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 * 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: General conceptual question about advantage of GPUs
Thank you, Justin. This is very helpful to me, especially the link to the GPU conference, which I think will be very helpful. I have done a little benchmarking on our ~7000 atom system, and in those tests the scaling was excellent -- almost linear when comparing 4, 8, 12, 16, 24 CPUs. I am using particle decomposition, though; the results might be different with domain decomposition, I guess. Thanks again. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] PTFE polymer chain
Hi I'm a new user of Gromacs and I want to construct a linear chain of polytetrafluoroethylene using the force field oplsaa. I created a work directory and I modified the rtp files by introducing 3 new residues corresponding to my starter of chain (TFEa), my internal residue (TFEi), and my terminal residue (TFEb)(following the same procedure descirbed by Justin for Polyethylene) I add these new three residue to the residuetypes.dat as Other. When I run pdb2gmx with the -ff option (for using my modified force field) the message of error is the following: Could not find force field '/home/user01/work/oplsaa.ff/' in current directory, install tree or GMXDATA path. If I use pdb2gmx without using the command -ff the error is always the same: Fatal error: Residue 'TFEa' not found in residue topology database How can I solve this problem? Could someone help me? Thanks! Luana. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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: General conceptual question about advantage of GPUs
On Tue, Apr 9, 2013 at 12:21 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Thank you, Justin. This is very helpful to me, especially the link to the GPU conference, which I think will be very helpful. I have done a little benchmarking on our ~7000 atom system, and in those tests the scaling was excellent -- almost linear when comparing 4, 8, 12, 16, 24 CPUs. I am using particle decomposition, though; the results might be different with domain decomposition, I guess. Yes, DD should be much faster than PD. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] PTFE polymer chain
On Tue, Apr 9, 2013 at 12:21 PM, luanadelore...@libero.it luanadelore...@libero.it wrote: Hi I'm a new user of Gromacs and I want to construct a linear chain of polytetrafluoroethylene using the force field oplsaa. I created a work directory and I modified the rtp files by introducing 3 new residues corresponding to my starter of chain (TFEa), my internal residue (TFEi), and my terminal residue (TFEb)(following the same procedure descirbed by Justin for Polyethylene) I add these new three residue to the residuetypes.dat as Other. When I run pdb2gmx with the -ff option (for using my modified force field) the message of error is the following: Could not find force field '/home/user01/work/oplsaa.ff/' in current directory, install tree or GMXDATA path. If I use pdb2gmx without using the command -ff the error is always the same: Fatal error: Residue 'TFEa' not found in residue topology database How can I solve this problem? Could someone help me? It would be helpful to see your exact command, because my suspicion is you're invoking pdb2gmx incorrectly (it looks like you're specifying a path, rather than just a base force field name). The modified .ff directory needs to be either in $GMXLIB or in the working directory. If you omit -ff altogether, pdb2gmx will detect it automatically and allow you to interactively choose it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] GROMACS 4.6 with GPU acceleration (double presion)
On 2013-04-09 18:06, Mikhail Stukan wrote: Dear experts, I have the following question. I am trying to compile GROMACS 4.6.1 with GPU acceleration and have the following diagnostics: # cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCUDA_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF CMake Error at cmake/gmxManageGPU.cmake:46 (message): GPU acceleration is not available in double precision! Call Stack (most recent call first): CMakeLists.txt:143 (include) Are there any plans to have double precision with GPU acceleration in the coming version of GROMACS or this will not happen in the nearest future. The hardware does not support it yet AFAIK. Thanks and regards, Mikhail -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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: installing CGenFF in Gromacs
I'll check out chapter 5. And look for those scripts that you mention. Thanks Justin! -- View this message in context: http://gromacs.5086.x6.nabble.com/installing-CGenFF-in-Gromacs-tp5007103p5007157.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 * 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: Re: [gmx-users] PTFE polymer chain
Please keep the discussion on the gmx-users list. On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it luanadelore...@libero.it wrote: Hi Justin, thansk for the fast reply. The exact command is this: pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don know if I made mistakes or simply I use bad the command. The command is incorrect. The -ff flag takes only the prefix of the force field you're trying to use. Your command is going to look for a directory called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put the custom oplsaa.ff directory in your working directory and issue pdb2gmx without the -ff flag. pdb2gmx will prompt you to choose the force field, allowing you to differentiate between oplsaa.ff in the working directory vs. the one in $GMXLIB. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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
R: Re: Re: [gmx-users] PTFE polymer chain
The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don't know if I made mistakes or simply I use badly the command. Thanks for the fast reply.Luana. Messaggio originale Da: jalem...@vt.edu Data: 09/04/2013 19.02 A: luanadelore...@libero.itluanadelore...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: Re: [gmx-users] PTFE polymer chain Please keep the discussion on the gmx-users list. On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it luanadelore...@libero.it wrote: Hi Justin,thansk for the fast reply. The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don know if I made mistakes or simply I use bad the command. The command is incorrect. The -ff flag takes only the prefix of the force field you're trying to use. Your command is going to look for a directory called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put the custom oplsaa.ff directory in your working directory and issue pdb2gmx without the -ff flag. pdb2gmx will prompt you to choose the force field, allowing you to differentiate between oplsaa.ff in the working directory vs. the one in $GMXLIB. -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 * 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] autocorrelation function of hydrogen bond : g_hbond
Is oscillation is because of change in hydrogen bonded distance? Do program consider the change in hydrogen bonded distance during ACF calculation? Nilesh There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that what you see? Erik On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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 * 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 * 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] autocorrelation function of hydrogen bond : g_hbond
No, this oscillation is related to libration. See, for instance http://www.princeton.edu/~fhs/rahman/rahman.pdf esp. Fig. 24 in this paper Best regards Paulo Netz On Tue, Apr 9, 2013 at 2:38 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Is oscillation is because of change in hydrogen bonded distance? Do program consider the change in hydrogen bonded distance during ACF calculation? Nilesh There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that what you see? Erik On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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 * 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 * 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 * 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] amber99 with berger's lipids
Did you correctly account for the different 1-4 scaling factors in the Berger and Amber lipids (either by obtaining .itp files from the authors of the Berger lipids-Amber protein article or making the changes yourself)? If not, then you are doing your simulation incorrectly (see their paper for why). Chris. -- original message -- By the way during simulation of the membrane-protein systems in the Amber99sb ff (with berger lipids) I've noticed decreased of my system in the Z-direction ( I've observed the same also during simulation of such systems in the Charm full atomic ff). In both cases the observed effect was seen in both GPU and non-gpu regimes with different cutoffs. It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff with berger lipids) I didnt observe such decreasing in the Z - dimension of my bilayer. The only difference was in the water models (spc in the gromos and tip3p in the amber or charm). Might it be relevant ? Should I switch to the spc water with the amber ? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] GPU performance
Good afternoon - I recently installed gromacs-4.6 on CentOS6.3 and the installation went just fine. I have a Tesla C2075 GPU. I then downloaded the benchmark directories and ran a bench mark on the GPU/ dhfr-solv-PME.bench This is what I got: Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible 1 GPU user-selected for this run: #0 Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' -1 steps, infinite ps. step 40: timed with pme grid 64 64 64, coulomb cutoff 1.000: 4122.9 M-cycles step 80: timed with pme grid 56 56 56, coulomb cutoff 1.143: 3685.9 M-cycles step 120: timed with pme grid 48 48 48, coulomb cutoff 1.333: 3110.8 M-cycles step 160: timed with pme grid 44 44 44, coulomb cutoff 1.455: 3365.1 M-cycles step 200: timed with pme grid 40 40 40, coulomb cutoff 1.600: 3499.0 M-cycles step 240: timed with pme grid 52 52 52, coulomb cutoff 1.231: 3982.2 M-cycles step 280: timed with pme grid 48 48 48, coulomb cutoff 1.333: 3129.2 M-cycles step 320: timed with pme grid 44 44 44, coulomb cutoff 1.455: 3425.4 M-cycles step 360: timed with pme grid 42 42 42, coulomb cutoff 1.524: 2979.1 M-cycles optimal pme grid 42 42 42, coulomb cutoff 1.524 step 4300 performance: 1.8 ns/day and from the nvidia-smi output: Tue Apr 9 10:13:46 2013 +--+ | NVIDIA-SMI 4.304.37 Driver Version: 304.37 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 Tesla C2075 | :03:00.0 On | 0 | | 30% 67CP080W / 225W | 4% 200MB / 5375MB | 4% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0 22568 mdrun 59MB | +-+ So I am only getting 1.8ns/day ! Is that right? It seems very very small compared to the CPU test where I am getting the same: step 200 performance: 1.8 ns/dayvol 0.79 imb F 14% From the md.log of the GPU test: Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2603 0 @ 1.80GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2a pic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 1 GPU detected: #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible 1 GPU user-selected for this run: #0 Will do PME sum in reciprocal space. Any thoughts as to why it is so slow? many thanks! Ben -- Research Assistant Professor North Carolina State University Department of Molecular and Structural Biochemistry 128 Polk Hall Raleigh, NC 27695 Phone: (919)-513-0698 Fax: (919)-515-2047 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] GPU performance
Hi Ben, That performance is not reasonable at all - neither for CPU only run on your quad-core Sandy Bridge, nor for the CPU+GPU run. For the latter you should be getting more like 50 ns/day or so. What's strange about your run is that the CPU-GPU load balancing is picking a *very* long cut-off which means that your CPU is for some reason performing very badly. Check how is mdrun behaving while running in top/htop nad if you are not seeing ~400% CPU utilization, there is something wrong - perhaps threads getting locked to the same core (to check that try -pin off). Secondly, note that you are using OpenMM-specific settings from the old GROMACS-OpenMM comparison benchmarks in which the grid spacing is overly coarse (you could use something like a fourier-spacing=0.125 or even larger with rc=1.0). Cheers, -- Szilárd On Tue, Apr 9, 2013 at 10:27 PM, Benjamin Bobay bgbo...@ncsu.edu wrote: Good afternoon - I recently installed gromacs-4.6 on CentOS6.3 and the installation went just fine. I have a Tesla C2075 GPU. I then downloaded the benchmark directories and ran a bench mark on the GPU/ dhfr-solv-PME.bench This is what I got: Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible 1 GPU user-selected for this run: #0 Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' -1 steps, infinite ps. step 40: timed with pme grid 64 64 64, coulomb cutoff 1.000: 4122.9 M-cycles step 80: timed with pme grid 56 56 56, coulomb cutoff 1.143: 3685.9 M-cycles step 120: timed with pme grid 48 48 48, coulomb cutoff 1.333: 3110.8 M-cycles step 160: timed with pme grid 44 44 44, coulomb cutoff 1.455: 3365.1 M-cycles step 200: timed with pme grid 40 40 40, coulomb cutoff 1.600: 3499.0 M-cycles step 240: timed with pme grid 52 52 52, coulomb cutoff 1.231: 3982.2 M-cycles step 280: timed with pme grid 48 48 48, coulomb cutoff 1.333: 3129.2 M-cycles step 320: timed with pme grid 44 44 44, coulomb cutoff 1.455: 3425.4 M-cycles step 360: timed with pme grid 42 42 42, coulomb cutoff 1.524: 2979.1 M-cycles optimal pme grid 42 42 42, coulomb cutoff 1.524 step 4300 performance: 1.8 ns/day and from the nvidia-smi output: Tue Apr 9 10:13:46 2013 +--+ | NVIDIA-SMI 4.304.37 Driver Version: 304.37 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 Tesla C2075 | :03:00.0 On | 0 | | 30% 67CP080W / 225W | 4% 200MB / 5375MB | 4% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0 22568 mdrun 59MB | +-+ So I am only getting 1.8ns/day ! Is that right? It seems very very small compared to the CPU test where I am getting the same: step 200 performance: 1.8 ns/dayvol 0.79 imb F 14% From the md.log of the GPU test: Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2603 0 @ 1.80GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2a pic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 1 GPU detected: #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible 1 GPU user-selected for this run: #0 Will do PME sum in reciprocal space. Any thoughts as to why it is so slow? many thanks! Ben -- Research Assistant Professor North Carolina State University Department of Molecular and Structural Biochemistry 128 Polk Hall Raleigh, NC 27695 Phone: (919)-513-0698 Fax: (919)-515-2047 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
Re: [gmx-users] GPU performance
Szilárd - First, many thanks for the reply. Second, I am glad that I am not crazy. Ok so based on your suggestions, I think I know what the problem is/was. There was a sander process running on 1 of the CPUs. Clearly GROMACS was trying to use 4 with Using 4 OpenMP thread. I just did not catch that. Sorry! Rookie mistake. Which I guess leads me to my next question (sorry if its too naive): (1) When running GROMACS (or a I guess any other CUDA based programs), its best to have all the CPUs free, right? I guess based on my results I have pretty much answered that question. Although I thought that as long as I have one CPU available to run the GPU it would be good: would setting -ntmpi 1 -ntomp 1 help or would I take a major hit in ns/day as well? If I try the benchmarks again just to see (for fun) with Using 4 OpenMP thread, under top I have - so I think the CPU is fine : PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 24791 bobayb20 0 48.3g 51m 7576 R 299.1 0.2 11:32.90 mdrun When I have a chance (after this sander run is done - hopefully soon) I can try the benchmarks again. Thanks again for the help! Ben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] GPU performance
On Apr 10, 2013 3:34 AM, Benjamin Bobay bgbo...@ncsu.edu wrote: Szilárd - First, many thanks for the reply. Second, I am glad that I am not crazy. Ok so based on your suggestions, I think I know what the problem is/was. There was a sander process running on 1 of the CPUs. Clearly GROMACS was trying to use 4 with Using 4 OpenMP thread. I just did not catch that. Sorry! Rookie mistake. Which I guess leads me to my next question (sorry if its too naive): (1) When running GROMACS (or a I guess any other CUDA based programs), its best to have all the CPUs free, right? I guess based on my results I have pretty much answered that question. Although I thought that as long as I have one CPU available to run the GPU it would be good: would setting -ntmpi 1 -ntomp 1 help or would I take a major hit in ns/day as well? Some codes might treat the CPU as a I/O, MPI and memory-serving co-processor of the GPU; those codes will tend to be insensitive to the CPU config. GROMACS goes to great lengths to use all the hardware in a dynamically load-balanced way, so CPU load and config tend to affect the bottom line immediately. Mark If I try the benchmarks again just to see (for fun) with Using 4 OpenMP thread, under top I have - so I think the CPU is fine : PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 24791 bobayb20 0 48.3g 51m 7576 R 299.1 0.2 11:32.90 mdrun When I have a chance (after this sander run is done - hopefully soon) I can try the benchmarks again. Thanks again for the help! Ben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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] General conceptual question about advantage of GPUs
Indeed. New players will benefit from http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html:-) Mark On Apr 9, 2013 5:59 PM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung adeyo...@andrew.cmu.edu wrote: Hi, For the past 2 years I have been running Gromacs on a standard Linux cluster (with nodes containing 24 CPUs). As you know, Gromacs scales excellently (and is super efficient), and since the CPUs are Intel Xeon 2.4 GHz processors, the simulations run quite fast (I can run 10 ns of ~7000 atoms in ~2 days on 24 CPUs). Can I expect GPUs to be any or much faster than these CPUs? You can try it out yourself for free and see: http://www.nvidia.com/object/gpu-test-drive.html?cid=gputestdrive I would expect better CPU performance, honestly. Have you done benchmarking on your system to see if fewer processors actually achieve better performance by eliminating some communication overhead? Using more processors is not necessarily better. There is a rumor in the department that GPUs can give a performance increase of 10-40 times relative to CPUs, although that group is using another MD package. I am curious whether this performance improvement is typical. (I would not expect it for Gromacs, though, since Gromacs is already super fast!) Relative speedup depends heavily upon what is being compared. Gromacs has a very fast baseline, so the relative speedup may not be as high as other codes that are not as intrinsically fast on CPU :) The GPU performance of Gromacs, in absolute terms, is very impressive. We run simulations of ~150,000 atoms on a single GPU card (which is somewhat outdated) and can achieve around 10 ns/day. Newer hardware would undoubtedly perform better. If you have time, do you know of any review or opinion papers that might discuss the advantages (advantages of performance or otherwise) of using GPUs over CPUs? Hopefully very soon, Erik's webinar from last week will be posted online ( http://www.gputechconf.com/page/gtc-express-webinar.html). I learned a lot from it, and I suspect others will as well. There is plenty of literature about GPU development in MD simulations, but again, be aware of unequal comparisons and baselines. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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 * 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] amber99 with berger's lipids
Mark, first of all I think that something wrong in amber and charm simulations because of some fluctuations of the box x-y-z dims during simulation Energy Average Err.Est. RMSD Tot-Drift --- Box-X 9.32108 0.0068 0.0360834 0.0289953 (nm) Box-Y 8.89245 0.0064 0.0344241 0.0276619 (nm) Box-Z 9.07051 0.013 0.0702945 -0.0525563 (nm) so due to decreasing of the box dims the overal conformational behaviour of the system is very 'straitjacketed' - its likely my protein placed in the compact crystal environment preventing its dynamics. James 2013/4/9 Mark Abraham mark.j.abra...@gmail.com On Tue, Apr 9, 2013 at 9:59 AM, James Starlight jmsstarli...@gmail.com wrote: By the way during simulation of the membrane-protein systems in the Amber99sb ff (with berger lipids) I've noticed decreased of my system in the Z-direction ( I've observed the same also during simulation of such systems in the Charm full atomic ff). In both cases the observed effect was seen in both GPU and non-gpu regimes with different cutoffs. It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff with berger lipids) I didnt observe such decreasing in the Z - dimension of my bilayer. The only difference was in the water models (spc in the gromos and tip3p in the amber or charm). Might it be relevant ? Should I switch to the spc water with the amber ? On principle, that is a bad idea. The force fields are parametrized to work with a particular water model, and you should only use another one after careful testing that there is a suitable benefit that outweighs any drawback. They are not plug and play. You have observed two different systems show different behaviour contracting in the Z direction. Why do you think one is abnormal and one is not? 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/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 * 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
