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normal XTC error when running MD

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11 years 3 months ago #1376 by AlexC
XTC error when running MD was created by AlexC
Dear All,

I'm having the following issue when I try to run MD on a system of peptides in water.

Program mdrun, VERSION 4.0.7
Source code file: stat.c, line: 348

Fatal error:
XTC error - maybe you are out of quota?

I tried changing xtc_grps to only the peptides, so to reduce the size of the .xtc output file, but this led to a segmentation fault.

I'm not sure what the issue was or how to solve it, but when I viewed the system in VMD I could see that in the final few frames one bead left the system entirely.We'd noticed a CoM issue before so I explicitly added both components of the system to comm_grps and this seems to have fixed the error.

Not sure if this is a suitable solution, so just wanted to run it past someone on here.

Thanks,
AlexC

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11 years 3 months ago #1377 by AlexC
Replied by AlexC on topic XTC error when running MD
UPDATE

This has worked for a short MD run of 50 steps, however when run for 500 steps there is a segmentation fault. The log file shows that the run stopped at step 234 where there was a large VCM error and a large increase in LJ energy.Steps 0, 233 and 234 are quoted below.

There are: 8130 Atoms
Max number of connections per atom is 9
Total number of connections is 2120
Max number of graph edges per atom is 2
Total number of graph edges is 640
Initial temperature: 300.054 K

Started mdrun on node 0 Tue Jan 22 11:53:46 2013

Step Time Lambda
0 0.00000 0.00000

Grid: 9 x 9 x 9 cells
Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
2.24517e+03 2.49930e+02 2.58434e+02 -2.17629e+05 -4.70155e+02
Potential Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
-2.15346e+05 3.04165e+04 -1.84929e+05 -1.84856e+05 3.00053e+02 1.26004e+04


Step Time Lambda
233 5.82500 0.00000

Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
1.89732e+03 2.53552e+02 4.86577e+02 -2.05079e+05 -4.23507e+02
Potential Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
-2.02865e+05 3.87429e+04 -1.64122e+05 -1.64352e+05 3.82191e+02 1.40151e+04


Step Time Lambda
234 5.85000 0.00000

Large VCM(group A6R): -22.07694, -14.59290, -33.99275, Temp-cm: 4.46645e+04
Large VCM(group W): 1.04788, 0.69265, 1.61347, Temp-cm: 1.00359e+02

Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
1.90189e+03 2.65279e+02 4.79953e+02 5.17992e+05 -4.20261e+02
Potential Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
5.20219e+05 8.87127e+09 8.87179e+09 8.87179e+09 8.75133e+07 1.34795e+08

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11 years 3 months ago #1379 by djurre
Replied by djurre on topic XTC error when running MD
I think this is more a question for the Gromacs mailing list. People there might answer your question faster.

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