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On 1/11/2011 3:43 AM, Yuri Garmay wrote:
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Try minimizing again now with all bonds constrained using the
output of the EM that ran. Generally, if EM crashes, your
system contains some unresolvable clash or inappropriate
geometry. Perhaps you have now relaxed the bad interactions
sufficiently to proceed.<br>
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<div>I had examined structure before first minimization and if
it was cause I would have been wondered. However I have tried
that advice, but this didn't solve the problem. Minimization
didn't crush, but didn't lead to any significant atom position
changes too.</div>
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It often doesn't.<br>
<br>
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<div> NPT position restrained simulation with all bonds
constrained crushes with minimized structure, but the same
with hbonds constrained doesn't. </div>
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Jumping straight to NPT is sometimes a bad idea. See <a
href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br>
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<div>The former produces exploded DMSO structures, the
latter produces visually correct trajectory. So, It seems that
structure is not the matter.</div>
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Your symptoms are consistent with a bad starting structure, wrong
topology or invalid preparation protocol. Nothing can be ruled out
yet.<br>
<br>
Mark<br>
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