[gmx-users] table extension
Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to nonbond_params pairs interactions which are specified in the TOP file (and also electrostatics)? Is there an interaction which does not use the table extension (other then bonds, angles dihdrals)? I have read the manual. Thanks, Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] molecule ouside water box
Hi gmx users, I defined an octahedral box with this line: $grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6 and then I solvated my protein with SPC water model: $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs I am now watching the trajectory of an MD simulation with a molecular visualisation software (VMD) and I noticed 2 unexpected things: 1) part of the molecule is outside the box 2) the box is cubic Although the molecule is out of the box, the periodic boundary conditions should ensure a correct behaviour, still, why is it cubic? Note: after solvation, the system was neutralised with genion, then an EM steep, an EM cg and a all-bonds constrained MD were performed before the actual MD. Any ideas? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule ouside water box
Stefano Meliga wrote: Hi gmx users, I defined an octahedral box with this line: $grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6 and then I solvated my protein with SPC water model: $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs I am now watching the trajectory of an MD simulation with a molecular visualisation software (VMD) and I noticed 2 unexpected things: 1) part of the molecule is outside the box 2) the box is cubic Although the molecule is out of the box, the periodic boundary conditions should ensure a correct behaviour, still, why is it cubic? Right, because in a periodic system, there is no outside, nor are there edges. The cubic appearance of the box is simply a visualization issue. You can retrieve your true box shape by using trjconv -pbc mol -ur compact. -Justin Note: after solvation, the system was neutralised with genion, then an EM steep, an EM cg and a all-bonds constrained MD were performed before the actual MD. Any ideas? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: HEME-cysteine gromacs simulation (zimohmily)
Thanks both Mark and chris.ne...@utoronto.ca 's advises. Listening to these words of yours,is better than learning for ten years. Most people uses the AMBER force field to run HEME simulation,I should focus on suitable force field and associated correct parameters.thanks 1. Re: HEME-cysteine gromacs simulation 2. HEME-cysteine gromacs simulation (chris.ne...@utoronto.ca) Message: 1(Mark Abraham) Date: Wed, 26 Aug 2009 12:46:24 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] HEME-cysteine gromacs simulation Visualization programs have to use heuristics to guess where bonds are and what names occur for which atoms (HG1 might be mercury or the first hydrogen on a gamma carbon, NE might be neon or an epsilon nitrogen, etc.). Only if you are able to read in a .tpr (such as with ngmx distributed inside GROMACS) can you get any visual confirmation of what GROMACS thinks you have described in your topology. There is no standardized widely-used mechanism for including such information in a PDB file, and so such usage of a file is unreliable. Read the .log files as well. GROMACS almost never segfaults (except when subjected to buggy MPI libraries), and when it does it will normally write some diagnostic information to stdout or the .log file. Sorry, I can't help there. please help me how handle those problems,how can i go on the simulation? Mark Message: 2 Date: Tue, 25 Aug 2009 23:10:17 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] HEME-cysteine gromacs simulation You always need a correct topology. The main issue here is that you need to have correct parameters. Where did you get your heme and Fe parameters? Were you careful about the Fe state oxidation state? I suspect that most people use Amber because of their antechamber program, which seems like a brilliant idea even if it may overstretch it's own parameterization without letting you know. I have no specific advice for you here beyond saying that it is worth spending a month figuring out what parameters you should really be using (hint: why would you be using ffG43a1 if most others use Amber here? do you know something that they don't?). This will end up saving you time in the long run. Note that ffG43a1 is the GROMOS forcefield, not the GROMACS forcefield. It is unfortunate that many programs (Amber, Charmm, gromacs) have their own similarly named forcefield, but that does not mean that the forcefield must be used with the associated program. There are forcefields that are not associated with a program (OPLS) and programs that never developed their own force field (NAMD, Desmond, Tinker, LAMMPS), so it is perfectly ok for you to use the amber forcefield with the gromacs program. Bottom line: read, read, read. Chris.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] table extension
Omer Markovitch wrote: Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to nonbond_params pairs interactions which are specified in the TOP file (and also electrostatics)? From 7.3.12, yes. These are the nonbonded interactions. Is there an interaction which does not use the table extension (other then bonds, angles dihdrals)? Probably not... if you're asking this question because you suspect something's not working properly, you might get enlightenment/a fix quicker if you're more explicit :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Converting pdb to Amber (to use with ffamber99)
Hi all, I am looking for a simple way to convert amino acid and nucleic residues from the PDB standard to the AMBER Nomenclature (to use with ffamber99 in GROMACS). Your help is appreciated. Nehme. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Converting pdb to Amber (to use with ffamber99)
Nehme El Hachem wrote: Hi all, I am looking for a simple way to convert amino acid and nucleic residues from the PDB standard to the AMBER Nomenclature (to use with ffamber99 in GROMACS). Your help is appreciated. Simple scripting (like Perl) or shell commands (vi, emacs editors or sed). -Justin Nehme. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Exploding poly-serine
Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form using TINKER, with neither end capped, then use pdb2gmx, editconv, genbox and genion to set the forcefield to OPLSAA/L, place it in a box of tip3p water, neutralized in a .096 M NaCl solution. I am trying to track down why this is occurring, and the first thing that seems suspicious is that the initial energy minimization run reaches convergence with a rather large force remaining on one of the atoms - the final statement from the EM run is: Steepest Descents converged to machine precision in 6793 steps, but did not reach the requested Fmax 10. Potential Energy = -4.9731194e+05 Maximum force = 7.1219537e+02 on atom 111 Norm of force = 6.5289087e+00 So I am thinking that with a large initial force on the polymer the system might be unrecoverably unstable and this is propagating through the subsequent steps of relaxing the water and the actual MD run to pop up as an explosion. If I look at the run log for the MD run, everything seems stable until the last step, at which point the temperature shoots up and the serine polymer explodes. Here are the last four steps from the run log: Step Time Lambda 208200 416.400020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.75158e+031.25586e+027.62176e+00 -6.45482e+01 1.16773e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80001e+036.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77043e+04 -3.15843e+051.01418e+063.17587e+02 -2.87690e+02 Step Time Lambda 208300 416.600020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.04345e+041.96147e+021.55806e+01 -3.31126e+01 1.24787e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80413e+036.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77229e+04 -3.14815e+051.02114e+063.17663e+02 -2.94492e+02 Step Time Lambda 208400 416.800020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 7.10106e+032.06975e+021.21357e+01 -2.52705e+01 1.16229e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.85247e+036.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.58806e+04 -3.19943e+051.02333e+063.10133e+02 -2.90942e+02 Step Time Lambda 208500 417.20.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.30968e+044.27637e+021.17359e+01 -5.59373e+01 1.39477e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80067e+036.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.03323e+05 -2.76511e+051.07569e+064.22292e+02 2.94766e+02 So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? Warren Gallin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exploding poly-serine
Warren Gallin wrote: Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form using TINKER, with neither end capped, then use pdb2gmx, editconv, genbox and genion to set the forcefield to OPLSAA/L, place it in a box of tip3p water, neutralized in a .096 M NaCl solution. I am trying to track down why this is occurring, and the first thing that seems suspicious is that the initial energy minimization run reaches convergence with a rather large force remaining on one of the atoms - the final statement from the EM run is: Steepest Descents converged to machine precision in 6793 steps, but did not reach the requested Fmax 10. Potential Energy = -4.9731194e+05 Maximum force = 7.1219537e+02 on atom 111 Norm of force = 6.5289087e+00 So I am thinking that with a large initial force on the polymer the system might be unrecoverably unstable and this is propagating through the subsequent steps of relaxing the water and the actual MD run to pop up as an explosion. If I look at the run log for the MD run, everything seems stable until the last step, at which point the temperature shoots up and the serine polymer explodes. Here are the last four steps from the run log: Step Time Lambda 208200 416.400020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.75158e+031.25586e+027.62176e+00 -6.45482e+011.16773e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80001e+036.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77043e+04 -3.15843e+051.01418e+063.17587e+02 -2.87690e+02 Step Time Lambda 208300 416.600020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.04345e+041.96147e+021.55806e+01 -3.31126e+011.24787e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80413e+036.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77229e+04 -3.14815e+051.02114e+063.17663e+02 -2.94492e+02 Step Time Lambda 208400 416.800020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 7.10106e+032.06975e+021.21357e+01 -2.52705e+011.16229e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.85247e+036.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.58806e+04 -3.19943e+051.02333e+063.10133e+02 -2.90942e+02 Step Time Lambda 208500 417.20.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.30968e+044.27637e+021.17359e+01 -5.59373e+011.39477e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80067e+036.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.03323e+05 -2.76511e+051.07569e+064.22292e+022.94766e+02 So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? What time step are you using? Since you are not using bond-constraints the time step should be on the order of 0.5 fs. Warren Gallin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list
Re: [gmx-users] LINCS
Hi Justin, I tried to run full MD after energy minimization in both vacuo and water... went good but I got this ERROR once I try to run full MD. Can you please help. = Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.014761, max 0.067846 (between atoms 416 and 417) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'VioLanthrone in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 336.210453, max 3218.528809 (between atoms 415 and 416) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 70 71 41.80.1530 0.2361 0.1530 69 70 121.00.1531 1.9697 0.1530 67 68 156.30.1624 8.0600 0.1530 66 67 64.60.1621 29.2909 0.1530 65 66 108.70.1578 35.0944 0.1530 64 65 72.80.1591 33.9603 0.1530 63 64 127.80.1603 5.8064 0.1530 61 62 131.80.1531 0.3537 0.1530 60 61 57.10.1530 0.1243 0.1530 286285 38.10.1368 0.1513 0.1360 284285 93.80.1385 0.3739 0.1360 283284 91.30.1443 1.0202 0.1390 282283 78.90.1452 7.6810 0.1390 281282 80.30.1448 9.0651 0.1390 279281 80.60.1446 3.3017 0.1390 279280 139.20.1440 0.7653 0.1390 278279 74.60.1430 11.7061 0.1390 278277 88.70.1423 9.9988 0.1390 276277 48.80.1410 1.5366 0.1390 275276 90.10.1396 4.7914 0.1390 274275 87.30.1405 18.6892 0.1390 273278 86.50.1423 6.0358 0.1390 273274 89.50.1413 19.8101 0.1390 271273 74.40.1422 6.3080 0.1390 271272 93.50.1258 8.1775 0.1230 270281 68.10.1445 2.5745 0.1390 270271 93.40.1431 8.6284 0.1390 270269 71.40.1414 1.5530 0.1390 268269 80.60.1406 6.4334 0.1390 267282 67.50.1443 25.7157 0.1390 267268 68.70.1427 28.0430 0.1390 266267 86.10.1436 72.5722 0.1390 266265 84.80.1422 222.9021 0.1390 264265 90.40.1408 390.2640 0.1390 263264 86.20.1415 393.1811 0.1390 261263 96.60.1433 30.2353 0.1390 261262 56.10.1257 22.0580 0.1230 260261 60.50.1428 22.8828 0.1390 260259 88.40.1411 1.0891 0.1390 257258 114.80.1394 0.3860 0.1390 256257 132.50.1399 0.2469 0.1390 255260 78.10.1426 1.3243 0.1390 255256 45.50.1414 0.7532 0.1390 253263 65.50.1447 32.5754 0.1390 252266 80.30.1448 71.8742 0.1390 252253 64.60.1449 14.7647 0.1390 251252 76.80.1449 18.2314 0.1390 254250 65.10.1428 1.7857 0.1390 249251 75.90.1440 2.1153 0.1390 249250 53.40.1426 0.1141 0.1390 249248 32.30.1388 0.1975 0.1360 438437 37.10.1366 0.1946 0.1360 436437 127.50.1377 2.6510 0.1360 434435 66.80.1428 4.2026 0.1390 433434 163.90.1415 2.0503 0.1390 436432 123.30.1406 2.7198 0.1390 420421 128.40.1398 2.1740 0.1390 419434 48.90.1421 1.2412 0.1390 418419 163.90.1432 18.4852 0.1390 418417 52.70.1431 31.4670 0.1390 416417 147.50.1484 136.8367 0.1390 415416 58.20.1449 447.5145 0.1390 413415 152.00.1475 331.5535 0.1390 413414 56.70.1261 283.8908 0.1230 412413 62.30.1446 272.3644 0.1390 412411 168.80.1449 54.1788 0.1390 409410 137.20.1402 4.5705 0.1390 408409 65.30.1430 1.8876 0.1390 407412 119.80.1459 25.1600 0.1390 407408 85.40.1446 14.0232 0.1390 406407 56.40.1469 17.4775 0.1390 405415 63.30.1460 430.7261 0.1390 405406 92.70.1471 85.9366 0.1390 404418 61.00.1462 49.7659 0.1390 404405 157.20.1470 116.1591 0.1390 403435 139.30.1448 26.6457 0.1390 406402 121.80.1454 5.0911 0.1390 401403 98.20.1445 23.9140 0.1390 401402 64.20.1449 0.5887 0.1390 401400 117.10.1385
Re: [gmx-users] LINCS
tekle...@ualberta.ca wrote: Hi Justin, I tried to run full MD after energy minimization in both vacuo and water... went good but I got this ERROR once I try to run full MD. Can you please help. There is something physically unrealistic about your model. That's the case whenever you see a LINCS warning. Without a more complete description of what you've done (minimization and equilibration protocol, initial construction of the model, etc) and the details of your simulation parameters, there's nothing more anyone can really say beyond a guess. It appears that the wiki is down at the moment, but these pages have useful information (when the site comes back up): http://oldwiki.gromacs.org/index.php/blowing_up http://oldwiki.gromacs.org/index.php/Errors And since LINCS errors have been posted thousands of times to the list, the archive should have some useful advice as well, so search here: http://oldwww.gromacs.org/swish-e/search/search2.php -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem in Energy minimisation for a rigid body system
Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four dummy atoms in the 4 corners of square plane. I could successfully equilibrate my system and proceed with my simulation. While trying to make my 5-site model, a rigid body, I constrained a bunch of distances between atoms by using the option constraints = all-bonds option in the .mdp file and also defining a bunch of improper dihedrals in .itp file. It worked perfectly and later I wanted to shift to my 7-site model. So in my old 5-site model, I just added another 2 dummy atoms, one above and another below the square plane. I tried to make it rigid by constraining another bunch of distances, the same way as I did it before. However, I'm not able to perform energy minimization, during which I receive LINCS WARNING messages. Can you please suggest me, where am I going wrong ? I'm pasting below the atoms and bonds directive of .itp file. [ atoms ] ; nr type resnr residu atom cgnr charge mass 1M1 1 SET M 1 0.0 53.380 2DZ1 1 SET D11 0.5 3.000 3DZ2 1 SET D21 0.5 3.000 4DZ3 1 SET D31 0.5 3.000 5DZ4 1 SET D41 0.5 3.000 6DZ5 1 SET D51-0.5 3.000 7DZ6 1 SET D61 0.5 3.000 [ bonds ] ; ai aj funct dist kb 1 2 1 0.06000267520.0 1 3 1 0.06000267520.0 1 4 1 0.06000267520.0 1 5 1 0.06000267520.0 2 3 1 0.08485267520.0 3 4 1 0.08485267520.0 4 5 1 0.08485267520.0 2 5 1 0.08485267520.0 1 6 1 0.02000267520.0 1 7 1 0.02000267520.0 2 6 1 0.06324267520.0 3 6 1 0.06324267520.0 4 6 1 0.06324267520.0 2 7 1 0.06324267520.0 3 7 1 0.06324267520.0 thanks Debasmita ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] is the D G sol of g_sas useless? why?
Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? Waiting for answer - Felipe Villanelo Lizana Biochemist Laboratorio de Biología Estructural y Molecular Universidad de Chile ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] is the D G sol of g_sas useless? why?
Felipe Villanelo wrote: Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? If you read it here, provide us a link :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exploding poly-serine
Warren Gallin wrote: David, That is probably it, I had a 2-femtosecond step and no bond constraints. Obviously I need to read up on the pros and cons of the various restraint regimes. I guess that would be consistent with the sudden explosion after along period of stable running. Why poly-Ser would be more susceptible to this than poly-Pro, poly-Asp or poly-Gly is not obvious to me, but I am sure that there is a reason out there somewhere. If this is the cause, the difference in numerical stability may well not be caused by the difference in the residue (i.e. the physical model) but in the initial conditions. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] wierd behavior of mdrun
I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in Energy minimisation for a rigid body system
dbis...@ucalgary.ca wrote: Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four dummy atoms in the 4 corners of square plane. I could successfully equilibrate my system and proceed with my simulation. While trying to make my 5-site model, a rigid body, I constrained a bunch of distances between atoms by using the option constraints = all-bonds option in the .mdp file and also defining a bunch of improper dihedrals in .itp file. It worked perfectly and later I wanted to shift to my 7-site model. So in my old 5-site model, I just added another 2 dummy atoms, one above and another below the square plane. I tried to make it rigid by constraining another bunch of distances, the same way as I did it before. However, I'm not able to perform energy minimization, during which I receive LINCS WARNING messages. Can you please suggest me, where am I going wrong ? I'm pasting below the atoms and bonds directive of .itp file. [ atoms ] ; nr type resnr residu atom cgnr charge mass 1M1 1 SET M 1 0.0 53.380 2DZ1 1 SET D11 0.5 3.000 3DZ2 1 SET D21 0.5 3.000 4DZ3 1 SET D31 0.5 3.000 5DZ4 1 SET D41 0.5 3.000 6DZ5 1 SET D51-0.5 3.000 7DZ6 1 SET D61 0.5 3.000 [ bonds ] ; ai aj funct dist kb 1 2 1 0.06000267520.0 1 3 1 0.06000267520.0 1 4 1 0.06000267520.0 1 5 1 0.06000267520.0 2 3 1 0.08485267520.0 3 4 1 0.08485267520.0 4 5 1 0.08485267520.0 2 5 1 0.08485267520.0 1 6 1 0.02000267520.0 1 7 1 0.02000267520.0 2 6 1 0.06324267520.0 3 6 1 0.06324267520.0 4 6 1 0.06324267520.0 2 7 1 0.06324267520.0 3 7 1 0.06324267520.0 If the symmetry of the system is to be octahedral, then you should try defining a symmetric set of bonds. You've omitted 5-6, 4-7 and 5-7. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] wierd behavior of mdrun
Paymon Pirzadeh wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Check that a short version of this job runs fine on a local machine. Probably you are having some problem with a file system and/or its buffering. Inspect your quotas. Talk to your system admins. Mark Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in Energy minimisation for a rigid body system
Hi Mark, Initially I included all the sets of bonds (as you have mentioned). Then I get the warning message while doing grompp, which says number of constraints is more (18 as I've defined) than required (it shouldn't be more than 15). With all the sets of bonds defined also, energy minimization didn't happen. Later I excluded 5-6, 4-7 and 5-7 from the list. However, nothing works. thanks dbis...@ucalgary.ca wrote: Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four dummy atoms in the 4 corners of square plane. I could successfully equilibrate my system and proceed with my simulation. While trying to make my 5-site model, a rigid body, I constrained a bunch of distances between atoms by using the option constraints = all-bonds option in the .mdp file and also defining a bunch of improper dihedrals in .itp file. It worked perfectly and later I wanted to shift to my 7-site model. So in my old 5-site model, I just added another 2 dummy atoms, one above and another below the square plane. I tried to make it rigid by constraining another bunch of distances, the same way as I did it before. However, I'm not able to perform energy minimization, during which I receive LINCS WARNING messages. Can you please suggest me, where am I going wrong ? I'm pasting below the atoms and bonds directive of .itp file. [ atoms ] ; nr type resnr residu atom cgnr charge mass 1M1 1 SET M 1 0.0 53.380 2DZ1 1 SET D11 0.5 3.000 3DZ2 1 SET D21 0.5 3.000 4DZ3 1 SET D31 0.5 3.000 5DZ4 1 SET D41 0.5 3.000 6DZ5 1 SET D51-0.5 3.000 7DZ6 1 SET D61 0.5 3.000 [ bonds ] ; ai aj funct dist kb 1 2 1 0.06000267520.0 1 3 1 0.06000267520.0 1 4 1 0.06000267520.0 1 5 1 0.06000267520.0 2 3 1 0.08485267520.0 3 4 1 0.08485267520.0 4 5 1 0.08485267520.0 2 5 1 0.08485267520.0 1 6 1 0.02000267520.0 1 7 1 0.02000267520.0 2 6 1 0.06324267520.0 3 6 1 0.06324267520.0 4 6 1 0.06324267520.0 2 7 1 0.06324267520.0 3 7 1 0.06324267520.0 If the symmetry of the system is to be octahedral, then you should try defining a symmetric set of bonds. You've omitted 5-6, 4-7 and 5-7. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
