Re: [gmx-users] Brownian Dynamics Simulations generating huge log files
I set nstlog = 1000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :( On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I am trying to simulate a system of 880 particles with implicit solvent >> using brownian dynamics, but the simulation generates huge log files (it >> writes md.log files at a rate of almost 5MB/minute) and this crashed my >> system since I ran out of space :( >> >> My mdp file looks like this: >> >> include = >> define = >> integrator = bd >> tinit= 0 >> dt = 0.001 >> nsteps = 1 ;10 >> simulation_part = 1 >> init_step= 0 >> comm-mode= Angular >> nstcomm = 1 >> comm-grps= >> >> emtol= 0.01 >> emstep = 1.5 >> >> nstxout = 1 >> nstvout = 1 >> nstfout = 1 >> >> nstenergy= 1000 >> >> nstxtcout= 1000 >> xtc-precision= 1000 >> >> nstlog = 0 >> >> xtc-grps = >> energygrps = >> >> ns_type = grid >> pbc = xyz >> periodic_molecules = no >> >> rlist= 8.95 >> >> coulombtype = user >> rcoulomb-switch = 0 >> rcoulomb = 8.95 >> epsilon-r= 1 >> >> vdw-type = user ;cutoff >> rvdw-switch = 0 >> rvdw = 8.95 >> DispCorr = No >> table-extension = 1 >> >> ; Seperate tables between energy group pairs >> energygrps = A T G C P300 SA SB >> >> >> energygrp_table = A A A T A G A C A P300 A SA A SB T T T >> G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA >> C SB P300 P300 P >> 300 SA P300 SB SA SA SA SB SB SB >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.10 >> >> Tcoupl = Nose-Hoover >> tc-grps = System >> tau_t= 0.001 >> > > This doesn't seem like a reasonable setting for tau_t; grompp should have > warned you about that since dt = tau_t! > > > ref_t= 300.00 >> >> Pcoupl = No >> >> andersen_seed= 815131 >> >> gen_vel = yes >> gen_temp = 300. >> gen_seed = 1993 >> >> Please let me know if there is a solution to write smaller mdp files. I >> have set nstlog = 0 , but even that doesn't work! >> > > Set nstlog to some incredibly large number, then, and it will only output a > few times. It seems strange that nstlog = 0 didn't suppress the .log file > output as it would any of the other nst* settings. > > -Justin > > >> Thanks >> Nimesh >> >> >> > -- > > > 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 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] Brownian Dynamics Simulations generating huge log files
Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlog = 0 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P300 SA SB energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P 300 SA P300 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.001 ref_t= 300.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 300. gen_seed = 1993 Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work! Thanks Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Log files
How do I turn off md.log fine generation in Gromacs? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Temperature Fluctuations
Hi, I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree apart. My system has implicit solvent and there is only one molecule in the system (around 270 atoms). I am using Nose-Hover thermostat and tabulated potentials. When I do simulations with exchange frequency of 1 ns, the system blows up and the temperature goes to a few 10,000K. When I remove RE, the temperature fluctuations are +/- 20 degrees and they increase with time. Does anyone know what the problem is ? Let me know if you need any other info about the system I am simulating. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: gro file and topology files
This [ molecules ] directive is at the end of the topology, right ? I was scared all my simulations went wrong. I have the correct order in molecules directive. [ molecules ] SS1 1 SS2 1 Neutral 536 Positive 137 Negative 71 The particles in gro file are in this order. Thank you! On Tue, Nov 9, 2010 at 12:37 PM, Justin A. Lemkul wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I was wondering if the order of molecules in topology file and the order >> of coordinates in gro file have to be same. My files are as follows: >> >> gro file: >> 1624 >>1B1 C1 22.237 30.408 26.522 >>1B1 SA2 22.348 30.033 26.829 >>1B1 P3 22.125 30.102 27.144 >>2B2 T4 21.852 30.069 26.468 >>2B2 SA5 21.824 30.189 26.949 >>2B2 P6 21.450 30.060 27.068 >>3B3 G7 21.778 29.762 26.361 >>3B3 SA8 21.321 30.008 26.724 >>3B3 P9 20.949 29.853 26.660 >>4B4 G 10 21.629 29.470 26.321 >>4B4 SA 11 21.026 29.716 26.325 >>4B4 P 12 20.750 29.499 26.117 >>5B5 A 13 21.487 29.154 26.338 >>5B5 SA 14 20.990 29.299 25.943 >>5B5 P 15 20.872 28.995 25.697 >>6B6 G 16 21.351 28.838 26.366 >>6B6 SA 17 21.165 28.798 25.747 >>6B6 P 18 21.201 28.428 25.579 >>7B7 A 19 21.229 28.513 26.410 >>7B7 SA 20 21.416 28.303 25.825 >>7B7 P 21 21.542 27.915 25.815 >>8B8 T 22 21.195 28.076 26.416 >>8B8 SA 23 21.574 27.883 26.158 >>8B8 P 24 21.640 27.516 26.330 >>9B9 A 25 20.912 27.888 26.523 >>9B9 SA 26 21.488 27.595 26.632 >>... >> ... upto 880 particles >> then, >> 295NEUNEU 881 27.530 28.268 24.349 >> 296NEUNEU 882 27.355 27.969 24.193 >> 297NEUNEU 883 27.623 27.876 23.941 >> 298NEUNEU 884 27.801 27.639 24.177 >> 299NEUNEU 885 27.473 27.507 24.322 >> 300NEUNEU 886 27.376 27.410 23.963 >> 301NEUNEU 887 27.316 26.930 24.121 >> 302NEUNEU 888 27.540 26.452 24.221 >> 303NEUNEU 889 27.266 26.353 23.979 >> 304NEUNEU 890 27.681 25.977 24.053 >> 305NEUNEU 891 27.538 25.708 24.281 >> . upto 1416 >> particles then, >> 831POSPOS 1417 27.764 28.400 24.075 >> 832POSPOS 1418 27.717 27.250 23.909 >> 833POSPOS 1419 27.466 26.805 23.792 >> 834POSPOS 1420 27.758 26.635 23.970 >> 835POSPOS 1421 27.530 26.183 23.770 >> 836POSPOS 1422 27.930 25.982 25.593 >> 837POSPOS 1423 27.940 25.614 25.687 >> 838POSPOS 1424 27.629 25.568 26.499 >> 839POSPOS 1425 27.293 25.195 26.653 >> 840POSPOS 1426 26.656 24.646 27.207 >> 841POSPOS 1427 27.493 24.378 26.671 >> 842POSPOS 1428 25.704 28.084 24.322 >> 843POSPOS 1429 26.024 28.033 24.522 >> 844POSPOS 1430 25.690 27.436 25.511 >> 845POSPOS 1431 25.499 26.486 25.378 >> ... upto 1553 >> particles then, >> 968NEGNEG 1554 27.665 27.041 24.226 >> 969NEGNEG 1555 27.770 25.717 24.582 >> 970NEGNEG 1556 27.165 25.469 26.884 >> 971NEGNEG 1557 26.602 25.231 27.215 >> 972NEGNEG 1558 27.309 24.502 27.300 >> 973NEGNEG 1559 27.075 25.317 25.083 >> 974NEGNEG 1560 26.927 25.837 25.127 >> 975NEGNEG 1561 26.247 26.641 24.480 >> 976NEGNEG 1562 25.888 26.676 24.614 >> 977NEGNEG 1563 25.773 27.276 25.174 >> 978NEGNEG 1564 25.345 26.065 25.614 >> 979NEGNEG 1565 24.862 26.307 25.737 >> 980NEGNEG 1566 27.642 26.470 26.780 >> 981NEGNEG 1567 26.721 27.065 26.145 >> 982NEGNEG 1568 26.398 26.984 25.969 >> 983NEGNEG 1569 26.291 25.493 26.397 >> 984NEGNEG 1570 26.029 24.681 26.249 >> 985NEGNEG 1571 26.374 23.945 26.814 >> 986NEGNEG 1572 26.551 24.207 25.873 >> 987NEGNEG 1573 27.184 23.760 24.934 >> 988NEGNEG 1574 25.102 22.440 25.649 >> 989NEGNEG 1575 23.763 24.119 26.999 >> ..1624 particles ... >> >> >&g
[gmx-users] RE: gro file and topology files
Hi, I was wondering if the order of molecules in topology file and the order of coordinates in gro file have to be same. My files are as follows: gro file: 1624 1B1 C1 22.237 30.408 26.522 1B1 SA2 22.348 30.033 26.829 1B1 P3 22.125 30.102 27.144 2B2 T4 21.852 30.069 26.468 2B2 SA5 21.824 30.189 26.949 2B2 P6 21.450 30.060 27.068 3B3 G7 21.778 29.762 26.361 3B3 SA8 21.321 30.008 26.724 3B3 P9 20.949 29.853 26.660 4B4 G 10 21.629 29.470 26.321 4B4 SA 11 21.026 29.716 26.325 4B4 P 12 20.750 29.499 26.117 5B5 A 13 21.487 29.154 26.338 5B5 SA 14 20.990 29.299 25.943 5B5 P 15 20.872 28.995 25.697 6B6 G 16 21.351 28.838 26.366 6B6 SA 17 21.165 28.798 25.747 6B6 P 18 21.201 28.428 25.579 7B7 A 19 21.229 28.513 26.410 7B7 SA 20 21.416 28.303 25.825 7B7 P 21 21.542 27.915 25.815 8B8 T 22 21.195 28.076 26.416 8B8 SA 23 21.574 27.883 26.158 8B8 P 24 21.640 27.516 26.330 9B9 A 25 20.912 27.888 26.523 9B9 SA 26 21.488 27.595 26.632 ... ... upto 880 particles then, 295NEUNEU 881 27.530 28.268 24.349 296NEUNEU 882 27.355 27.969 24.193 297NEUNEU 883 27.623 27.876 23.941 298NEUNEU 884 27.801 27.639 24.177 299NEUNEU 885 27.473 27.507 24.322 300NEUNEU 886 27.376 27.410 23.963 301NEUNEU 887 27.316 26.930 24.121 302NEUNEU 888 27.540 26.452 24.221 303NEUNEU 889 27.266 26.353 23.979 304NEUNEU 890 27.681 25.977 24.053 305NEUNEU 891 27.538 25.708 24.281 . upto 1416 particles then, 831POSPOS 1417 27.764 28.400 24.075 832POSPOS 1418 27.717 27.250 23.909 833POSPOS 1419 27.466 26.805 23.792 834POSPOS 1420 27.758 26.635 23.970 835POSPOS 1421 27.530 26.183 23.770 836POSPOS 1422 27.930 25.982 25.593 837POSPOS 1423 27.940 25.614 25.687 838POSPOS 1424 27.629 25.568 26.499 839POSPOS 1425 27.293 25.195 26.653 840POSPOS 1426 26.656 24.646 27.207 841POSPOS 1427 27.493 24.378 26.671 842POSPOS 1428 25.704 28.084 24.322 843POSPOS 1429 26.024 28.033 24.522 844POSPOS 1430 25.690 27.436 25.511 845POSPOS 1431 25.499 26.486 25.378 ... upto 1553 particles then, 968NEGNEG 1554 27.665 27.041 24.226 969NEGNEG 1555 27.770 25.717 24.582 970NEGNEG 1556 27.165 25.469 26.884 971NEGNEG 1557 26.602 25.231 27.215 972NEGNEG 1558 27.309 24.502 27.300 973NEGNEG 1559 27.075 25.317 25.083 974NEGNEG 1560 26.927 25.837 25.127 975NEGNEG 1561 26.247 26.641 24.480 976NEGNEG 1562 25.888 26.676 24.614 977NEGNEG 1563 25.773 27.276 25.174 978NEGNEG 1564 25.345 26.065 25.614 979NEGNEG 1565 24.862 26.307 25.737 980NEGNEG 1566 27.642 26.470 26.780 981NEGNEG 1567 26.721 27.065 26.145 982NEGNEG 1568 26.398 26.984 25.969 983NEGNEG 1569 26.291 25.493 26.397 984NEGNEG 1570 26.029 24.681 26.249 985NEGNEG 1571 26.374 23.945 26.814 986NEGNEG 1572 26.551 24.207 25.873 987NEGNEG 1573 27.184 23.760 24.934 988NEGNEG 1574 25.102 22.440 25.649 989NEGNEG 1575 23.763 24.119 26.999 ..1624 particles ... topology ... ... [ moleculetype ] Neutral1 [ atoms ] 1 NEU 1 NEU NEU1 [ moleculetype ] Positive1 [ atoms ] 1 POS 1 POS POS1 [ moleculetype ] Negative1 [ atoms ] 1 NEG 1 NEG NEG1 [ moleculetype ] SS11 [ atoms ] 1C1 B1C 1 2 SA1 S1 SA 2 3P1 P1P 3 4T2 B2T 4 5 SA2 S2 SA 5 6P2 P2P 6 7G3 B3G 7 8 SA3 S3 SA 8 9P3 P3P 9 10G4 B4G 10 11 SA4 S4 SA 11 12P4 P4P 12 13A5 B5A 13 14 SA5 S5 SA 14 The starting coordinates in gro file belong to molecule SS1 in topology file. As you can see, the coordinates for NEU, POS and NEG particles are towards the end in gro file but I am defining these particles in the beginning of topology file. Please let me know if this is ok or is it wrong ? And how can I check. Thanks, Nimesh -
[gmx-users] RE: Error in mdrun
Hi, I keep getting the following error when I do mdrun: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. I moved the particles sufficiently apart so that there are no overlaps. I still get this error. Can someone tell me what else can I do? Please let me know if you need any other info. Thanks, Nimesh -- 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] Restart Replica Exchange
Hi, I was wondering if anyone knows whether it is possible to restart a replica exchange simulation if it stops during the run. I tried it once before and got the error that all the replicas should be at the same time step for replica exchange. When I checked the time step of different replicas, there was a few 10s of picoseconds difference b/w them. Is there a way to circumvent this problem and restart replica exchange? Thanks, Nimesh -- 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: Molecule out of pbc box
Hi, Does anyone know if there is a way to put a molecule back in the pbc box in gromacs. I am visualizing my sims in vmd and the molecule keeps going out of the box. Is it normal or an artifact in vmd, is there a way to put the molecule back in the box? please let me know. Thanks, Nimesh -- 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: Targeted MD
Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is this sufficient or are there any other things that I need to consider. Also, I have tabulated potentials. If any one knows how to do this, or if you need more info on my system, please let me know. Thanks, Nimesh -- 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] RE: log files
Well, no. I got a 20GB log file when nstlog was 1000. When I changed it to 1, the log file was about 1 MB after a few minutes of simulation which means that it will be in GBs in a few days. On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel wrote: > You've set the frequency of writing to log file as > 'nstlog = 10'. > Given that 'nsteps = 1', you're writing to the > log file only 1000 times. Do you get a 20GB md.log file with these settings? > > -Gaurav > > On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain < > nimeshjain2...@u.northwestern.edu> wrote: > >> Hi, >> >> I am having some problem in my simulations related to log files. The file >> sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log >> file. One of my grompps looks like this: >> [tau_t is very low because I am using bd and it doesn't work otherwise]. >> [I am doing a replica exchange with 10,000 as exchange frequency] >> >> >> include = >> define = >> integrator = bd >> tinit= 0 >> dt = 0.001 >> nsteps = 1 ;10 >> simulation_part = 1 >> init_step= 0 >> comm-mode= Angular >> nstcomm = 1 >> comm-grps= >> >> >> emtol= 0.01 >> emstep = 1.5 >> >> nstxout = 1 >> nstvout = 1 >> nstfout = 1 >> >> nstlog = 10 >> nstenergy= 1000 >> >> nstxtcout= 1000 >> xtc-precision= 1000 >> >> xtc-grps = >> energygrps = >> >> ns_type = grid >> pbc = xyz >> periodic_molecules = no >> >> rlist= 8.95 >> >> coulombtype = user >> rcoulomb-switch = 0 >> rcoulomb = 8.95 >> >> epsilon-r= 1 >> >> vdw-type = user ;cutoff >> rvdw-switch = 0 >> rvdw = 8.95 >> DispCorr = No >> table-extension = 1 >> ; Seperate tables between energy group pairs >> energygrps = A T G C P260 SA SB >> >> energygrp_table = A A A T A G A C A P260 A SA A SB T T T >> G T C T P260 T S >> A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB P260 P260 >> P260 SA P260 SB >> SA SA SA SB SB SB >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.10 >> >> Tcoupl = Nose-Hoover >> tc-grps = System >> tau_t= 0.0001 >> ref_t= 260.00 >> >> Pcoupl = No >> >> andersen_seed= 815131 >> >> gen_vel = yes >> gen_temp = 260. >> gen_seed = 1993 >> >> ; ENERGY GROUP EXCLUSIONS >> ; Pairs of energy groups for which all non-bonded interactions are >> excluded >> energygrp_excl = >> >> >> >> Please let me know if anyone knows whats the problem. >> >> Thanks, >> Nimesh >> >> -- >> 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 > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern 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/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: log files
Hi, I am having some problem in my simulations related to log files. The file sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log file. One of my grompps looks like this: [tau_t is very low because I am using bd and it doesn't work otherwise]. [I am doing a replica exchange with 10,000 as exchange frequency] include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 10 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P260 SA SB energygrp_table = A A A T A G A C A P260 A SA A SB T T T G T C T P260 T S A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB P260 P260 P260 SA P260 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.0001 ref_t= 260.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 260. gen_seed = 1993 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = Please let me know if anyone knows whats the problem. Thanks, Nimesh -- 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 Replica Exchange
My time step is 1 fs. And the md0.log doesn't have anything about replica exchange which I suppose means that its not doing replica exchange. In my other simulation, (100 ns duration and 1 fs time step), replica exchange is initialized but the exchange frequency is 10^9 (so I am not actually doing a replica exchange, but I have the conditions for that.) Is it possible that the parallel replicas can go to different time steps during the simulation if the simulation is a replica exchange one but no exchanges are attempted during the duration of the simulation. Thanks for the help. All suggestions were really helpful. Thanks, Nimesh On Tue, Aug 3, 2010 at 10:23 AM, David van der Spoel wrote: > On 2010-08-03 17.17, Nimesh Jain wrote: > >> And the simulation is for 100ns. >> > So you are trying exchanges ecery 2 ns (assuming 2 fs timestep). That is > rather long. If you check the file md0.log you can see whether the repl. > exch. code is initialized at all. If that is the case then I guess you are > seeing output file buffering (check dates on your files: the shorter ones > should be older). If not something else is wrong. > >> >> On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain >> > <mailto:nimeshjain2...@u.northwestern.edu>> wrote: >> >>mdrun command I am using: (I have a shell script that adds jobs on >>the server) Following are the contents of that: >> >>#!/bin/bash >># >>#$ -cwd >>#$ -j y >>#$ -S /bin/bash >>#$ -pe mpi 8 >> >>echo $TMP > info1 >> >>unset SGE_ROOT >> >>cp $TMP/machines . >> >>MPI_DIR=/opt/openmpi/ >> >>$MPI_DIR/bin/mpirun -np $NSLOTS -machinefile $PWD/machines \ >> /share/apps/gromacs-4.0.5/bin/mdrun_mpi \ >> -s topol_.tpr -multi 8 -pd replex 100 >> >> >>Thanks, >>Nimesh >> >> >> >>On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel >>mailto:sp...@xray.bmc.uu.se>> wrote: >> >>On 2010-08-03 17.08, Nimesh Jain wrote: >> >>Hi, >> >>I am doing a replica exchange simulation with 8 replicas. I >>was looking >>at my data and I observed that a couple of replicas are >>around 10 and 20 >>ns ahead of everything else. Is it normal or is this wrong ? >>Please let me know. >> >>Thanks, >>Nimesh >> >>What frequency of exchange do you use? >>Please give mdrun command line >> >>-- >>David van der Spoel, Ph.D., Professor of Biology >>Dept. of Cell & Molec. Biol., Uppsala University. >>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> >>http://folding.bmc.uu.se >>-- >>gmx-users mailing list gmx-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 >> >> >> >> >> >> >> -- >> Nimesh Jain >> Graduate Student >> Biomedical Engineering >> Northwestern University >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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 > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern 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/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 Replica Exchange
And the simulation is for 100ns. On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain < nimeshjain2...@u.northwestern.edu> wrote: > mdrun command I am using: (I have a shell script that adds jobs on the > server) Following are the contents of that: > > #!/bin/bash > # > #$ -cwd > #$ -j y > #$ -S /bin/bash > #$ -pe mpi 8 > > echo $TMP > info1 > > unset SGE_ROOT > > cp $TMP/machines . > > MPI_DIR=/opt/openmpi/ > > $MPI_DIR/bin/mpirun -np $NSLOTS -machinefile $PWD/machines \ > /share/apps/gromacs-4.0.5/bin/mdrun_mpi \ > -s topol_.tpr -multi 8 -pd replex 100 > > > Thanks, > Nimesh > > > > On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel > wrote: > >> On 2010-08-03 17.08, Nimesh Jain wrote: >> >>> Hi, >>> >>> I am doing a replica exchange simulation with 8 replicas. I was looking >>> at my data and I observed that a couple of replicas are around 10 and 20 >>> ns ahead of everything else. Is it normal or is this wrong ? >>> Please let me know. >>> >>> Thanks, >>> Nimesh >>> >>> What frequency of exchange do you use? >> Please give mdrun command line >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in Replica Exchange
mdrun command I am using: (I have a shell script that adds jobs on the server) Following are the contents of that: #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash #$ -pe mpi 8 echo $TMP > info1 unset SGE_ROOT cp $TMP/machines . MPI_DIR=/opt/openmpi/ $MPI_DIR/bin/mpirun -np $NSLOTS -machinefile $PWD/machines \ /share/apps/gromacs-4.0.5/bin/mdrun_mpi \ -s topol_.tpr -multi 8 -pd replex 100 Thanks, Nimesh On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel wrote: > On 2010-08-03 17.08, Nimesh Jain wrote: > >> Hi, >> >> I am doing a replica exchange simulation with 8 replicas. I was looking >> at my data and I observed that a couple of replicas are around 10 and 20 >> ns ahead of everything else. Is it normal or is this wrong ? >> Please let me know. >> >> Thanks, >> Nimesh >> >> What frequency of exchange do you use? > Please give mdrun command line > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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] Problem in Replica Exchange
Hi, I am doing a replica exchange simulation with 8 replicas. I was looking at my data and I observed that a couple of replicas are around 10 and 20 ns ahead of everything else. Is it normal or is this wrong ? Please let me know. Thanks, Nimesh -- 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] Free Energy Calculation Using Tabulated Potentials
Hi, I am having some troubles calculating free energies. Can someone please tell me if I have tabulated potentials, can I calculate free energy using the gromacs options in the mdp file for free energies. (If someone has done it, can you please provide a sample topology file.) Thanks, Nimesh -- 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
