RE: molecules distorted

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Mar 22 2005 - 15:37:19 CST

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Do you have your input files? Perhaps you have to carry out a better
energy minimization procedure.
Michel

-----Original Message-----
From: Samuel Flores [mailto:samuel.flores_at_yale.edu]
Sent: Tuesday, March 22, 2005 3:35 PM
To: Michel Espinoza-Fonseca; 'Brian Bennion'
Cc: namd-l_at_ks.uiuc.edu
Subject: molecules distorted

Howdy all,

Many thanks for answers to previous questions. I am now visualizing the
results of an MD run of a protein in a water sphere. A few of the atoms
are
distorted, though, as if thrown completely out of place at an early time
step. Is there some sort of close-contact removal run I should be
doing?
I've already tried reducing the time step.

Any help would be appreciated.

Sam

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