[gmx-users] continue replica exchange MD
Erik Marklund
erikm at xray.bmc.uu.se
Thu Mar 22 16:15:29 CET 2012
22 mar 2012 kl. 08.05 skrev lina:
> On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:
>> Hello,
>>
>> Upon continuing a replica exchange MD simulation using the command
>>
>> mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 10000 -cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e edrRemd_20ns.edr -stepout 2000
>
>> From my side, I have no problem resuming or extending the REMD
> simulations in V.4.5.5 and 4.5.4
I've had problems with continuation of REMD simulations with gmx 4.5.5 (although manifested differently IIRC). The release-4-5-patches contain bugfixes that solved the problems. I suggest trying the patches.
Erik
>
> Here is the command:
>
> mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append
>
> ^^^^^^^^ I use state_.cpt, not state.cpt
>
>>
>> I get the following output:
>> **************************************
>> ...
>> ...
>> 5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps).
>> 5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps).
>>
>> step 49430, will finish Wed Sep 12 16:09:33 2012
>> step 50000, will finish Thu May 24 11:23:04 2012
>> Step 47546: resetting all time and cycle counters
>>
>> =>> PBS: job killed: walltime 604823 exceeded limit 604800
>> Terminated
>> ******************************************
>>
>> Apparently, the job runs for one week on a computer cluster (that is the maximum time allowed), but it does not progress very much beyond step 49430.
>>
>> Also the log-file does not show any more steps:
>> ************************************************
>> Step Time Lambda
>> 46455 92.91000 0.00000
>>
>> Grid: 18 x 17 x 25 cells
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
>> 5.83095e+04 3.70277e+04 2.14102e+03 8.83853e+03 -7.33070e+02
>> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
>> 2.29503e+05 3.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06
>> Coul. recip. Position Rest. Potential Kinetic En. Total Energy
>> -9.59421e+05 5.41532e+03 -3.09689e+06 5.18959e+05 -2.57793e+06
>> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
>> 2.97550e+02 -1.14933e+02 5.41944e+01 0.00000e+00
>>
>> Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
>>
>> -----------------------------------------------------------
>> Restarting from checkpoint, appending to previous log file.
>> ...
>> ...
>> Started mdrun on node 0 Tue Mar 6 16:40:10 2012
>>
>> Step Time Lambda
>> 49430 98.86000 0.00000
>>
>> Grid: 18 x 17 x 25 cells
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
>> 5.84241e+04 3.69121e+04 2.09533e+03 8.80916e+03 -4.67086e+02
>> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
>> 2.29528e+05 2.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06
>> Coul. recip. Position Rest. Potential Kinetic En. Total Energy
>> -9.59506e+05 5.47116e+03 -3.09823e+06 5.18993e+05 -2.57923e+06
>> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
>> 2.97570e+02 -1.14963e+02 2.67842e+00 0.00000e+00
>>
>> Step Time Lambda
>> 50000 100.00000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
>> 5.86161e+04 3.71585e+04 2.15336e+03 8.92946e+03 -4.84684e+02
>> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
>> 2.29950e+05 3.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06
>> Coul. recip. Position Rest. Potential Kinetic En. Total Energy
>> -9.59537e+05 5.56712e+03 -3.09531e+06 5.19371e+05 -2.57594e+06
>> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
>> 2.97787e+02 -1.14956e+02 2.36460e+01 1.50068e-05
>> [End of log-file]
>> ***********************************
>>
>> I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem or maybe a problem of the computer cluster (MPI, etc). I would be grateful for any help.
>>
>> Many thanks
>> Andreas--
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
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