Hi Justin,
I think it is the minimization issue. I did steep for 2000 steps, and it
works thereafter for the mdrun, for this structure.
Thank you very much!
Regards,
Stone Gao
--------------------------------------------------
From: "Justin A. Lemkul" <jalem...@vt.edu>
Sent: Tuesday, September 01, 2009 4:35 PM
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: Re: [gmx-users] mdrun running without simulating new steps
st wrote:
Hi,
I run a two-molecule system with mdrun_d in a water box (~10000 water
molecules.)
The program looks running properly (no errors nor warnnings)
However the program seems stop outputting files (because the output file
size stop increases) after about 5min.
The mdrun_d interface looks normal without any errors, the md.log
contains only two saves:
<snip>
Grid: 9 x 9 x 14 cells
Energies (kJ/mol)
Bond Morse Angle G96Angle Proper
Dih.
3.35232e+05 3.27635e+01 7.09937e+02 1.73811e+01
2.47097e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic
En.
1.48669e+05 -4.50390e+05 -1.89304e+04 1.78117e+04
4.38796e+05
Total Energy Conserved En. Temperature Pressure (bar)
4.56608e+05 4.56608e+05 1.09892e+03 -5.74950e+04
Step Time Lambda
100 0.05000 0.00000
Energies (kJ/mol)
Bond Morse Angle G96Angle Proper
Dih.
3.38536e+05 1.06967e+03 2.21584e+04 4.26526e+01
3.13457e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic
En.
8.73487e+04 -5.64854e+05 -4.48577e+04 -1.57422e+05
3.56524e+05
Total Energy Conserved En. Temperature Pressure (bar)
1.99102e+05 7.60608e+05 8.92881e+02 7.56563e+04
I'd say the system is exploding. Your temperature is oscillating between
1000 K and 893 K using a Nose-Hoover thermostat, and your potential starts
off in excess of 10^4 kJ mol^-1. Did you run any sort of energy
minimization or weak-coupling equilibration before this run?
It's odd that mdrun wouldn't give some sort of LINCS warning or write out
step*.pdb files right beforehand, though.
-Justin
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--
========================================
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
========================================
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