[gmx-users] Segmentation fault

[Sayan Bagchi]

Hello All,

I was trying to run a MD simulation of a 17 amino acid peptide. At the
position restraint step, the program crashed after running ~536 ps.

It gave the error message:

"t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.
Check for bad contacts and/or reduce the timestep. Wrote pdb files with
previous and current coordinates."

So I looked into the pdb files for atom 6101:

In the last but one step, the pdb file looks like:

ATOM   6101  OW  SOL  1970      44.896  30.613  17.849  1.00  0.00
ATOM   6102  HW1 SOL  1970      45.375  30.296  18.668  1.00  0.00
ATOM   6103  HW2 SOL  1970      44.264  29.904  17.537  1.00  0.00

In the last step, the pdb file looks like:

ATOM   6101  OW  SOL  1970
395154652137521152.000-290190255628222464.000695407981780533248.000  1.00
0.00
ATOM   6102  HW1 SOL  1970
-2104656020830683136.0005806908484133847040.000-6427192471385538560.000
1.00  0.00
ATOM   6103  HW2 SOL  1970
1131095442881249280.000593978790032441344.0001018902650772520960.000  1.00
0.00

So, there is clearly something wrong. What should I do now to solve this
problem?

Thanks,
Sayan.

-- 
 Sayan Bagchi
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