Minimization problem on cluster

From: Swarna M Patra (
Date: Mon Oct 04 2010 - 23:11:41 CDT

Hi Namd users,

I have been using namd for the last few years . this problem is something I
am facing now. Earlier I was using some different computational facility. I
have a system (protein + lipid +water +ions). I have 3 clusters.
If I run on cluster A ---- no problem
If I run on cluster B ---- after 500 + steps of minimization nothing
happens, even if I leave it long time it shows running in queue but no
If I run on cluster C ----- it gives ver huge nos in energy like
99999999999999 and it never comes down.

What could be the problem? why the same system behave like this on different
clusters. Please give me some suggestions as now cluster A is down how do I
run my system.


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