[gmx-users] LINCS crushes
Mark.Abraham at anu.edu.au
Tue Nov 1 01:53:27 CET 2011
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
> 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
> 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.
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