I did not use -shuffle -t to run this. However even when I use -shuffle
option the same error occurs.
From: Sridhar Acharya <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: [gmx-users] MD continuation runs in serial but not in parallel
Date: Mon, 03 Jul 2006 17:56:27 +0530
Dear GMX users,
I used grompp with -t option to continue a serially run simulation to run
in parallel. I have given gen_vel = no in the .mdp file.
But mdrun "with -np 2" stops and reports the following error. (md.log file
is given below)
The same simulation could be continued in serial without any error.
What is the cause for this descrepancy? Any parameters to be set?
#########################################################################################
Going to use C-settle (5335 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra =
0.00645837
rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1
Constraining the coordinates at t0-dt (step -1)
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.000042 4862 4887 0.000007
After LINCS 0.000049 4880 4881 0.000010
Started mdrun on node 0 Mon Jul 3 18:48:47 2006
Initial temperature: 301.39 K
Grid: 17 x 14 x 19 cells
Step Time Lambda Annealing
0 0.00000 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.058480 3573 3574 0.005918
After LINCS 0.000140 3842 3844 0.000020
t = 0.000 ps: Water molecule starting at atom 17176 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
8.10484e+03 3.58568e+03 2.61866e+03 1.41412e+03 4.86285e+04
LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.
2.14166e+08 -5.54411e+05 -1.31762e+05 2.13544e+08 nan
Total Energy Temperature Pressure (bar)
nan nan nan
##############################################################################################
--
Did you use the -shuffle option of grompp?
With grompp -shuffle -t
grompp expectes a shuffled trajectory.
Berk.
--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: [EMAIL PROTECTED]
Phone: Lab: 08413-235467*2044
Mobile: 9866147193
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