Re: [gmx-users] Which .tpr file to use for g_rms?
On 4/12/2010 6:45 PM, Anirban Ghosh wrote: Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump Did you read trjconv -h about -pbc nojump? Notice how when you didn't give your command lines last time, you didn't get a very useful answer. So which .tpr file should I use? You're trying to measure a membrane thickness. So you want all the membrane residues in the same box, and don't care about anything else. There's various ways to use -pbc and -center to achieve this, depending on what the simulation has done. Mark Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are. Mark Thanks again. Anirban On 12/4/10, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org
[gmx-users] two graphene sheets are blowing up
Hi ALL, I am using GMX4.5.3. I have done a system, which include two graphenes and a CNT. I put two graphenes at both end of the CNT,and dig a hole to let water pass through CNT. I do not change any force fileld . I just treat all the carbon atoms as atoms in Benzene ring CA in AMBER03 force filed. But I find a problem, I must freeze all the carbon atoms in the graphenes, and then do the NVT equilibrium, so I can not do NPT equilibrium. If I use positon restraint instead of freezing the graphenes, the two graphenes will be blowing up., and a series of warnings about LINCS , and the simulation stop. I want to use positon restraint and do NPT equilibrium and MD. Anybody could help me, thanks a lot ! Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.114658, max 1.034921 (between atoms 670 and 672) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.111497, max 1.026519 (between atoms 1013 and 1014) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1485 1487 37.50.1376 0.1519 0.1400 615617 37.10.1376 0.1510 0.1400 1881 1882 37.00.1376 0.1516 0.1400 1487 1536 44.00.1375 0.1542 0.1400 1011 1012 37.30.1376 0.1513 0.1400 1534 1536 46.40.1355 0.1429 0.1400 1536 1538 38.60.1350 0.1439 0.1400 1440 1489 46.80.1356 0.1436 0.1400 1538 1540 93.60.1377 0.2631 0.1400 1489 1882 43.30.1376 0.1540 0.1400 1540 1542 92.70.1389 0.2830 0.1400 1489 1491 39.10.1350 0.1432 0.1400 1542 1591 40.80.1391 0.1742 0.1400 1491 1883 93.50.1378 0.2645 0.1400 1589 1591 38.00.1386 0.1267 0.1400 1495 1544 36.40.1386 0.1262 0.1400 617666 42.70.1375 0.1533 0.1400 1544 1884 43.70.1391 0.1771 0.1400 664666 45.70.1355 0.1426 0.1400 1883 1884 92.60.1390 0.2801 0.1400 666668 38.10.1350 0.1437 0.1400 570619 45.80.1356 0.1422 0.1400 668670 93.60.1377 0.2647 0.1400 619 1012 43.10.1376 0.1534 0.1400 670672 92.70.1389 0.2849 0.1400 619621 38.90.1350 0.1446 0.1400 672721 40.70.1391 0.1743 0.1400 621 1013 93.60.1377 0.2652 0.1400 719721 37.70.1386 0.1269 0.1400 625674 38.10.1386 0.1261 0.1400 674 1014 42.30.1391 0.1749 0.1400 1013 1014 92.60.1390 0.2837 0.1400 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.040717, max 0.154305 (between atoms 1171 and 1172) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.039914, max 0.153441 (between atoms 207 and 255) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1019 1021 58.50.1376 0.1350 0.1400 1021 1863 41.20.1379 0.1494 0.1400 1021 1023 48.20.1363 0.1476 0.1400 149151 57.10.1376 0.1340 0.1400 151993 41.40.1379 0.1493 0.1400 151153 47.40.1363 0.1471 0.1400 1065 1067 54.90.1366 0.1379 0.1400 1067 1116 45.50.1359 0.1460 0.1400 1067 1069 40.40.1377 0.1498 0.1400 195197 54.70.1367 0.1370 0.1400 197246 44.80.1360 0.1461 0.1400 197199 39.30.1377 0.1496 0.1400 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.350444, max 2.603891 (between atoms 195 and 197) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 6.990928, max 43.715271 (between atoms 570 and 619) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 7.147569, max 45.401707 (between atoms 1534 and 1536) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1479 1527 31.40.1179 0.1637 0.1400 1389 1391 71.80.1350 0.4267 0.1400 Step 1, time 0.002 (ps) LINCS WARNING relative constraint
Re: [gmx-users] two graphene sheets are blowing up
On 4/12/2010 7:48 PM, zhongjin wrote: Hi ALL, I am using GMX4.5.3. I have done a system, which include two graphenes and a CNT. I put two graphenes at both end of the CNT,and dig a hole to let water pass through CNT. I do not change any force fileld . I just treat all the carbon atoms as atoms in Benzene ring CA in AMBER03 force filed. I don't understand what dig a hole means but it sounds like you're leaving some carbon valences unfilled, which will probably destabilize things, leading to www.gromacs.org/Documentation/Terminology/Blowing_Up Mark But I find a problem, I must freeze all the carbon atoms in the graphenes, and then do the NVT equilibrium, so I can not do NPT equilibrium. If I use positon restraint instead of freezing the graphenes, the two graphenes will be blowing up., and a series of warnings about LINCS , and the simulation stop. I want to use positon restraint and do NPT equilibrium and MD. Anybody could help me, thanks a lot ! Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.114658, max 1.034921 (between atoms 670 and 672) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.111497, max 1.026519 (between atoms 1013 and 1014) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1485 1487 37.50.1376 0.1519 0.1400 615617 37.10.1376 0.1510 0.1400 1881 1882 37.00.1376 0.1516 0.1400 1487 1536 44.00.1375 0.1542 0.1400 1011 1012 37.30.1376 0.1513 0.1400 1534 1536 46.40.1355 0.1429 0.1400 1536 1538 38.60.1350 0.1439 0.1400 1440 1489 46.80.1356 0.1436 0.1400 1538 1540 93.60.1377 0.2631 0.1400 1489 1882 43.30.1376 0.1540 0.1400 1540 1542 92.70.1389 0.2830 0.1400 1489 1491 39.10.1350 0.1432 0.1400 1542 1591 40.80.1391 0.1742 0.1400 1491 1883 93.50.1378 0.2645 0.1400 1589 1591 38.00.1386 0.1267 0.1400 1495 1544 36.40.1386 0.1262 0.1400 617666 42.70.1375 0.1533 0.1400 1544 1884 43.70.1391 0.1771 0.1400 664666 45.70.1355 0.1426 0.1400 1883 1884 92.60.1390 0.2801 0.1400 666668 38.10.1350 0.1437 0.1400 570619 45.80.1356 0.1422 0.1400 668670 93.60.1377 0.2647 0.1400 619 1012 43.10.1376 0.1534 0.1400 670672 92.70.1389 0.2849 0.1400 619621 38.90.1350 0.1446 0.1400 672721 40.70.1391 0.1743 0.1400 621 1013 93.60.1377 0.2652 0.1400 719721 37.70.1386 0.1269 0.1400 625674 38.10.1386 0.1261 0.1400 674 1014 42.30.1391 0.1749 0.1400 1013 1014 92.60.1390 0.2837 0.1400 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.040717, max 0.154305 (between atoms 1171 and 1172) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.039914, max 0.153441 (between atoms 207 and 255) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1019 1021 58.50.1376 0.1350 0.1400 1021 1863 41.20.1379 0.1494 0.1400 1021 1023 48.20.1363 0.1476 0.1400 149151 57.10.1376 0.1340 0.1400 151993 41.40.1379 0.1493 0.1400 151153 47.40.1363 0.1471 0.1400 1065 1067 54.90.1366 0.1379 0.1400 1067 1116 45.50.1359 0.1460 0.1400 1067 1069 40.40.1377 0.1498 0.1400 195197 54.70.1367 0.1370 0.1400 197246 44.80.1360 0.1461 0.1400 197199 39.30.1377 0.1496 0.1400 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.350444, max 2.603891 (between atoms 195 and 197) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 6.990928, max 43.715271 (between atoms 570 and 619) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 7.147569,
[gmx-users] MOPAC gromacs mdreun error
Dear gmx users i have successfuly installed Mopac gromacs/interface. but when i run the QM/MM in mdrun_d i have got hte following error QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! Segmentation fault (core dumped) i am using 6 atoms for my Qm region i am using fedora core13 OS and pentium intel i5 what could i do to remove this error ? i am expecting your reply soon thanks in advance -- 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] Ramachandran plot for non standar residues
Hello, I am trying to calculate the Ramachandran plot for a molecules based on non-standar aminoacids, parametrized with the Gaff force field and simulated with Gromacs 4.0.7. When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy I get: Found 0 phi-psi combinations. I suppose the problem is the nomenclature of my atoms, since I don´t have any CA named atoms. Is there any way to calculate g_rama for non-standar residues defining the atoms I need? Thanks a lot for your help. Best whishes, Rebeca Garcia Santiago de Compostela University Spain -- 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] Ramachandran plot for non standar residues
Rebeca García Fandiño wrote: Hello, I am trying to calculate the Ramachandran plot for a molecules based on non-standar aminoacids, parametrized with the Gaff force field and simulated with Gromacs 4.0.7. When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy I get: Found 0 phi-psi combinations. I suppose the problem is the nomenclature of my atoms, since I don´t have any CA named atoms. Is there any way to calculate g_rama for non-standar residues defining the atoms I need? I think you can just change the atom names in your topology, generate a new .tpr file, and run g_rama again. I don't believe atom names are stored in the trajectory. -Justin Thanks a lot for your help. Best whishes, Rebeca Garcia Santiago de Compostela University Spain -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Desktop Freezes While Using mdrun-gpu
Hello friends, I'm writing today to see if anyone could offer further insight/commentary than the current available documentation and comments from the program itself concerning the following problem. I am currently using mdrun-gpu, v 4.5.3, utilizing my GPU, an NVIDIA GeForce GT 330M. When I run the program, my desktop freezes, though I am able to move my cursor about. I can hear the fan growing louder and the computer heating up, as it always does when I use the CPU mdrun. Browsing the available documentation, I recognize that my particular GPU is not listed as one of the tested. However, from reading further, and from the error codes generated by mdrun-gpu, I am suspect that it is possible to use a GPU not listed in the manual, so long as the other requirements (such as the use of the OpenMM library) are met. Could anyone who is using the GPU version perhaps offer some insight into what is occurring and any potential fixes that may be successful? I would be most appreciative? Also, if I haven't provided enough information, I'm more than happy to answer any questions quickly and succinctly to do so! Many thanks for any help anyone can provide! Best, Solomon Berman Department of Chemistry Boston 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] [OT] Generate random coil protein conformations?
Hi, Sorry for the offtopic but my google-fu is apparently abandoning me. I am looking for a fast way to generate random coil protein configurations to use as startpoints for several simulations I'd like to do. All I managed to find is: - FOLDTRAJ which seems unavailable and discontinued - the server at unfolded.uchicago.edu, which actual working part ( http://z-appserver.cti.depaul.edu/~unfolded/start.html ) seems unavailable as well. Anyone has working suggestions for that? I am quite sure there must be such a package, yet I can't find it... dumb me probably. cheers, M. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] [OT] Generate random coil protein conformations?
On 12/05/10, ms deviceran...@gmail.com wrote: Hi, Sorry for the offtopic but my google-fu is apparently abandoning me. I am looking for a fast way to generate random coil protein configurations to use as startpoints for several simulations I'd like to do. All I managed to find is: - FOLDTRAJ which seems unavailable and discontinued - the server at unfolded.uchicago.edu, which actual working part ( http://z-appserver.cti.depaul.edu/~unfolded/start.html ) seems unavailable as well. Anyone has working suggestions for that? I am quite sure there must be such a package, yet I can't find it... dumb me probably. I dunno if it will help, but Googling with self-avoiding Gaussian walk might help - since that's what a random coil is. 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
Re: [gmx-users] [OT] Generate random coil protein conformations?
On 05/12/10 00:26, Mark Abraham wrote: Sorry for the offtopic but my google-fu is apparently abandoning me. I am looking for a fast way to generate random coil protein configurations to use as startpoints for several simulations I'd like to do. All I managed to find is: - FOLDTRAJ which seems unavailable and discontinued - the server at unfolded.uchicago.edu, which actual working part ( http://z-appserver.cti.depaul.edu/~unfolded/start.html ) seems unavailable as well. Anyone has working suggestions for that? I am quite sure there must be such a package, yet I can't find it... dumb me probably. I dunno if it will help, but Googling with self-avoiding Gaussian walk might help - since that's what a random coil is. Thanks, nice tip -even if I doubt that a real RC is truly Gaussian in angle distribution, it is good enough for what I want to do -I can script Pymol about that. m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] dna, lipid simulation
Hi all, This is a question unrelated to gromacs but would pose it anyway to get some hints from the experts. I wish to set up DNA and DPPC lipid membrane simulation. Could someone please refer to a relevant forcefield/tutorial for simulation of lipids with DNA? Any help will be really appreciated. Thank you amit -- 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
