[gmx-users] MD continuation runs in serial but not in parallel

[Sridhar Acharya]

I did not use -shuffle -t  to run this. However even when I use -shuffle 
option the same error occurs.

>>From: Sridhar Acharya <sridharfirst at gmail.com>
>>Reply-To: sridhar at cdfd.org.in,Discussion list for GROMACS users 
>><gmx-users at gromacs.org>
>>To: gmx-users at 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: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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