On 1/11/2011 3:43 AM, Yuri Garmay wrote:
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.
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.
It often doesn't.
NPT position restrained simulation with all bonds constrained crushes
with minimized structure, but the same with hbonds constrained doesn't.
Jumping straight to NPT is sometimes a bad idea. See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
The former produces exploded DMSO structures, the
latter produces visually correct trajectory. So, It seems that
structure is not the matter.
Your symptoms are consistent with a bad starting structure, wrong
topology or invalid preparation protocol. Nothing can be ruled out yet.
Mark
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