Re: [gmx-users] linc warnings
subarna thakur wrote: Hi, I am using the following keywords in pr.mdp file for the simulation for protein with fe4s4 cluster; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 150; total 3000 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps= ProteinNon-Protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps= Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the Fe4s4 cluster atoms are showing large rms and rotating hugely in position restraining step and Linc warnings are comming. In some published papers it is mentioned that during the molecular dynamics simulations, the proteins' heavy atoms and the counter ions were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? That's what position restraints are doing. Watch the trajectory, and see if you can find where things are going wrong. If the crash is happening reasonably early, you can set nstxout = 1 to get a bunch of frames right before the crash. Perhaps there are some atomic clashes that are still unresolved after EM. The Fmax you achieved before is indeed quite high. Have a look around atom 820 and see where the clash might be. Another possibility for the instability of your system is of course inappropriate parameters in the topology. How have you parameterized the Fe4S4 cluster? MM force fields generally fail spectacularly for such transition metal species, especially with the quantum effects (charge transfer, etc) present in such systems. Have you seen the following? http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin subarna *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, 29 December, 2009 5:44:03 PM *Subject:* Re: [gmx-users] linc warnings subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force= 1.7402682e+03 on atom 820 Norm of force= 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together If EM worked nicely, then something else you are doing is incorrect. snip the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms.. Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings? Without seeing your .mdp file and perhaps even snippets of your topology pertaining to the Fe4S4 cluster, there's nothing else to say except please read the standard advice: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality.
Re: [gmx-users] linc warnings
Justin A. Lemkul wrote: snip were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? That's what position restraints are doing. I should amend this slightly. I assumed your Fe4S4 cluster was simply part of your protein, which is restrained with posre.itp, generated by pdb2gmx. If this is not the case, you will have to use genrestr to generate a position restraint file for the Fe4S4 cluster, if it is indeed a separate molecule type. I doubt that restraining the Fe4S4 cluster will fix anything. Please see my last message - there are clashes in your system or inappropriate parameters at play. If you restrain the atoms, you may be just delaying the inevitable crash. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some molecule clashing with another ?
Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database ( vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? 2. how to find the clashed molecules ? Thank you Lin -- 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] some molecule clashing with another ?
Chih-Ying Lin wrote: Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. You can change probable to an actual answer if you analyze whatever LINCS warnings are occurring (the atoms are listed) and by watching the resulting trajectory. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand Then you should follow up #4 above with another visual inspection, as you did with protein-ligand interactions, in addition to any information printed to the log file (as above). = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database (vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. So solvent-solvent overlap shouldn't be a problem. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) Yes, this is standard. ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? In theory, not really. What values of potential energy and maximum force did the energy minimization converge to? 2. how to find the clashed molecules ? Read the information printed to the log file (again, I'm assuming you're seeing LINCS warnings, but you haven't told us what broke means!) and watch the trajectory to see where things start to fall apart. As I suggested to someone earlier, if the crash is happening reasonably early, setting nstxout = 1 is a useful diagnostic to capture all frames prior to the crash. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some molecule clashing with another ?
Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? Thank you Lin Step -2, time -0.002 (ps) *LINCS WARNING* relative constraint deviation after LINCS: max 0.044043 (between atoms 366 and 368) rms 0.001724 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 366367 36.80.1973 0.1301 0.1250 366368 36.60.1963 0.1305 0.1250 starting mdrun 'HEN EGG WHITE LYSOZYME in water' 5000 steps, 5.0 ps. Step 0, time 0 (ps) *LINCS WARNING *relative constraint deviation after LINCS: max 42.623165 (between atoms 1499 and 1518) rms 2.341352 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1376 1377 39.10.1470 0.1471 0.1470 1404 1405 59.80.1430 0.2374 0.1430 1405 1406 88.50.1530 0.2358 0.1530 1406 1407 76.60.1530 0.1851 0.1530 1407 1408 74.30.1531 0.2407 0.1530 1438 1439 34.80.1530 0.1557 0.1530 1439 1440 34.40.1530 0.1594 0.1530 1499 1518 90.00.1090 4.7549 0.1090 1554 1578 90.00.1090 0.2729 0.1090 1594 1595 53.50.1390 0.1650 0.1390 1595 1596 57.10.1390 0.1515 0.1390 1595 1615 90.30.1090 0.5874 0.1090 1666 1652 48.50.1392 0.1535 0.1390 1654 1678 90.10.1092 0.4554 0.1090 1656 1679 90.20.1092 0.1300 0.1090 1657 1680 90.00.1092 1.6346 0.1090 1660 1661 58.00.1393 0.1424 0.1390 1661 1662 54.50.1392 0.1467 0.1390 1661 1681 88.90.1091 0.1237 0.1090 1665 1684 89.80.1091 0.3454 0.1090 1667 1666 53.10.1531 0.1364 0.1530 Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1# Back Off! I just backed up 6LYZ-PR.trr to ./#6LYZ-PR.trr.1# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 *346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 *373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 1045 1046 47.00.1780 0.1783 0.1780 1118 1119 36.80.1090 0.1069 0.1090 1128 1129 31.80.1000 0.1019 0.1000 1130 1131 35.60.1340 0.1334 0.1340 1152 1153 89.60.1530 0.2937 0.1530 1153 1154 90.30.1529 2.2321 0.1530 1154 1155 89.90.1529 7.7561 0.1530 1155 1156 90.30.1470 8.2649 0.1470 1156 1157 60.60.1000 0.1543 0.1000 1156 1158 49.60.1339 0.1783 0.1340 1158 1159 48.40.1340 0.1038 0.1340 1159 1160 86.40.1000 0.1375 0.1000 1165 1166 45.80.1230 0.1207 0.1230 Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3# Sorry couldn't backup
Re: [gmx-users] some molecule clashing with another ?
Chih-Ying Lin wrote: Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? No, you can conclude that your system is unstable. One possible reason is atomic clashing, but you cannot say for sure. General advice on your problem (which is encountered frequently, and as such, appears thousands of times in the list archive) can be found on the Gromacs wiki site: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want further help, take the advice that I gave you before - look at the trajectory, focusing specifically on the problematic atoms (looks like 366 and 367 are having problems first, suggesting that either they, or atoms nearby, are unstable). I also asked about the success of your energy minimization, but you haven't provided that information. From the output, it seems that your simulation is crashing immediately, suggesting that EM did not work properly, and there *may* be unresolved clashes. You will have to do visual inspection to determine if this is the case. -Justin Thank you Lin Step -2, time -0.002 (ps) *LINCS WARNING* relative constraint deviation after LINCS: max 0.044043 (between atoms 366 and 368) rms 0.001724 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 366367 36.80.1973 0.1301 0.1250 366368 36.60.1963 0.1305 0.1250 starting mdrun 'HEN EGG WHITE LYSOZYME in water' 5000 steps, 5.0 ps. Step 0, time 0 (ps) *LINCS WARNING *relative constraint deviation after LINCS: max 42.623165 (between atoms 1499 and 1518) rms 2.341352 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1376 1377 39.10.1470 0.1471 0.1470 1404 1405 59.80.1430 0.2374 0.1430 1405 1406 88.50.1530 0.2358 0.1530 1406 1407 76.60.1530 0.1851 0.1530 1407 1408 74.30.1531 0.2407 0.1530 1438 1439 34.80.1530 0.1557 0.1530 1439 1440 34.40.1530 0.1594 0.1530 1499 1518 90.00.1090 4.7549 0.1090 1554 1578 90.00.1090 0.2729 0.1090 1594 1595 53.50.1390 0.1650 0.1390 1595 1596 57.10.1390 0.1515 0.1390 1595 1615 90.30.1090 0.5874 0.1090 1666 1652 48.50.1392 0.1535 0.1390 1654 1678 90.10.1092 0.4554 0.1090 1656 1679 90.20.1092 0.1300 0.1090 1657 1680 90.00.1092 1.6346 0.1090 1660 1661 58.00.1393 0.1424 0.1390 1661 1662 54.50.1392 0.1467 0.1390 1661 1681 88.90.1091 0.1237 0.1090 1665 1684 89.80.1091 0.3454 0.1090 1667 1666 53.10.1531 0.1364 0.1530 Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1# Back Off! I just backed up 6LYZ-PR.trr to ./#6LYZ-PR.trr.1# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 *346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.7
[gmx-users] How to modify or avoid some molecule clashing with another ?
Hi After reading the log file and watching the trajectory movies(nstxout = 1), some molecule clashes with another in my simulation system. How can i avoid the situation happening again? How to modify the broken simulation? Thank you Lin Message: 4 Date: Wed, 30 Dec 2009 19:00:51 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] some molecule clashing with another ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b3be9b3.8020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. You can change probable to an actual answer if you analyze whatever LINCS warnings are occurring (the atoms are listed) and by watching the resulting trajectory. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand Then you should follow up #4 above with another visual inspection, as you did with protein-ligand interactions, in addition to any information printed to the log file (as above). = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database (vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. So solvent-solvent overlap shouldn't be a problem. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) Yes, this is standard. ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? In theory, not really. What values of potential energy and maximum force did the energy minimization converge to? 2. how to find the clashed molecules ? Read the information printed to the log file (again, I'm assuming you're seeing LINCS warnings, but you haven't told us what broke means!) and watch the trajectory to see where things start to fall apart. As I suggested to someone earlier, if the crash is happening reasonably early, setting nstxout = 1 is a useful diagnostic to capture all frames prior to the crash. -Justin Thank you Lin -- 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 (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to modify or avoid some molecule clashing with another ?
Chih-Ying Lin wrote: Hi After reading the log file and watching the trajectory movies(nstxout = 1), some molecule clashes with another in my simulation system. How can i avoid the situation happening again? How to modify the broken simulation? Two options come to mind: 1. Re-generate the molecule coordinates by using the -seed option of genbox when inserting the molecules into the unit cell. 2. If the clash is between a ligand molecule and a solvent molecule, you could just delete the problematic water molecule and update the topology accordingly. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some molecule clashing with another ?
Hi I print out the energy EM-solvated.edr file here. Since the average is high, is it caused by the molecule clashing? I selected potential, kinetic, total energy. What else energy should I print out to learn the broken simulation system? Thank you Lin Select the terms you want from the following list by selecting either the name or the number or a combination. End your selection with an empty line or a zero. - 1 Bond 2 G96Bond3 Angle 4 G96Angle 5 Proper-Dih.6 Improper-Dih. 7 LJ-14 8 Coulomb-14 9 LJ-(SR)10 Coulomb-(SR) 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Temperature15 Pressure-(bar) 16 Vir-XX 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ 25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) 29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) 33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y 37 Mu-Z 38 T-rest 11 12 13 0 Back Off! I just backed up 6LYZ-EM-solvated.xvg to ./#6LYZ-EM-solvated.xvg.2# Last frame read 41 time 65.000 Statistics over 65 steps [ 1. thru 65. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 Kinetic En. 0 0 0 0 0 Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 gcq#119: Bring Out the Gimp (Pulp Fiction) Chih-Ying Lin wrote: Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? No, you can conclude that your system is unstable. One possible reason is atomic clashing, but you cannot say for sure. General advice on your problem (which is encountered frequently, and as such, appears thousands of times in the list archive) can be found on the Gromacs wiki site: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want further help, take the advice that I gave you before - look at the trajectory, focusing specifically on the problematic atoms (looks like 366 and 367 are having problems first, suggesting that either they, or atoms nearby, are unstable). I also asked about the success of your energy minimization, but you haven't provided that information. From the output, it seems that your simulation is crashing immediately, suggesting that EM did not work properly, and there *may* be unresolved clashes. You will have to do visual inspection to determine if this is the case. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] some molecule clashing with another ?
Chih-Ying Lin wrote: Hi I print out the energy EM-solvated.edr file here. Since the average is high, is it caused by the molecule clashing? It means there's something badly wrong. For the usual sort of biomolecular MD simulation, PE should be negative, around 10^-4 to 10^-6 kJ/mol depending on force field and system size. Thus in your case, at least one contribution is probably very large and positive. If you look at all the contributions to the energy (easiest in your .log file), you will see that the LJ is very large and positive (go check it!) which can only happen when atoms are unrealistically close to each other. I selected potential, kinetic, total energy. What else energy should I print out to learn the broken simulation system? Work out what the terms are, and then use your chemical to knowledge to see if any of them are meaningful here :-) Mark Thank you Lin Select the terms you want from the following list by selecting either the name or the number or a combination. End your selection with an empty line or a zero. - 1 Bond 2 G96Bond3 Angle 4 G96Angle 5 Proper-Dih.6 Improper-Dih. 7 LJ-14 8 Coulomb-14 9 LJ-(SR)10 Coulomb-(SR) 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Temperature15 Pressure-(bar) 16 Vir-XX 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ 25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) 29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) 33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y 37 Mu-Z 38 T-rest 11 12 13 0 Back Off! I just backed up 6LYZ-EM-solvated.xvg to ./#6LYZ-EM-solvated.xvg.2# Last frame read 41 time 65.000 Statistics over 65 steps [ 1. thru 65. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 Kinetic En. 0 0 0 0 0 Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 gcq#119: Bring Out the Gimp (Pulp Fiction) Chih-Ying Lin wrote: Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? No, you can conclude that your system is unstable. One possible reason is atomic clashing, but you cannot say for sure. General advice on your problem (which is encountered frequently, and as such, appears thousands of times in the list archive) can be found on the Gromacs wiki site: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want further help, take the advice that I gave you before - look at the trajectory, focusing specifically on the problematic atoms (looks like 366 and 367 are having problems first, suggesting that either they, or atoms nearby, are unstable). I also asked about the success of your energy minimization, but you haven't provided that information. From the output, it seems that your simulation is crashing immediately, suggesting that EM did not work properly, and there *may* be unresolved clashes. You will have to do visual inspection to determine if this is the case. -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] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- 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] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? Don't know. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Yeah probably. You need to understand what LINCS does to make some sense of this output. It doesn't really matter though. A well-behaved simulation will have none of these warnings. Atoms 366 and 368 are connected by a constraint and unhappy at the start of the simulation. In the output you quote, their distance has gone from under 1nm to a ridiculous number. Look at the region of those atoms in the starting configuration, and work out why. The most likely hypothesis is that some other atom is so close to them that they experienced a massive force, and had massive LJ. Mark Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- 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] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? It corresponds to the length between the constrained atoms. Forces are printed to the .trr file if you have set nstfout 0. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? The constraint length at the previous step and the current one. Judging by the size of these values, it means your system is exploding hopelessly, as the constrained bond is currently at nearly infinite length. -Justin is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] clashing happened inside the protein molecule?
Hi Here is my .out file. atoms 366 and 368 are two atoms inside the protein. What is other possible way to solve it ? Thank you Lin relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 -- 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] Break ? = Position restrained MD
Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move. I checked the .out file. The max is happened on the atoms inside protein. Why? Thank you Lin -- 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] Break ? = Position restrained MD
Chih-Ying Lin wrote: Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move... appreciably under normal conditions. However if you have a medium restraining force and a ridiculously large LJ force, guess who wins? I checked the .out file. The max is happened on the atoms inside protein. Why? Probably because they were overlapping with some other atoms initially. Try setting up a simpler simulation system until you work out how to get things right. Definitely record each step as you do it (e.g. copy and paste your terminal history after using history) so you know what you're doing where. 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] gromacs 4.06 binary for linux -redhat
Hi I am new to GROMACS, like to use it. I would be appreciate if anyone can direct me to the right place where I could get the linux binary either x32/x64 - redhat. I could not compile the source cause it is looking for FFTW etc.,. thanks venkat -- 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] gromacs 4.06 binary for linux -redhat
venkat wrote: Hi I am new to GROMACS, like to use it. I would be appreciate if anyone can direct me to the right place where I could get the linux binary either x32/x64 - redhat. Binaries for newer versions probably haven't been made yet. Your subject line points to version 4.0.6, which was a broken release anyway, and was replaced by version 4.0.7. I could not compile the source cause it is looking for FFTW etc.,. Then you should follow the step-by-step installation instructions. FFT libraries are a prerequisite for Gromacs. Please see the following: http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions -Justin thanks venkat -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
