Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished

From: David A Case <>
Date: Thu, 16 Jul 2015 08:36:58 -0400

On Thu, Jul 16, 2015, Vahid Kshani wrote:
> Then we have changed, dt = 0.001 and the heating is taken place without
> any error, but the structure is distorting too much (kindly see the
> attached figure). We appreciate your suggestions and comments.

There is very little information to go on here. You have some long bonds
in the structure in your figure. Identify the atoms involved, and look to see
if that helps you debug the problem. Make sure the box dimensions (in the
"Ewald parameters" section of the mdout file) are correct. Use the
"checkvalidity" command in (or the "checkoverlap" command in
cpptraj) to look for problems with your system setup.


AMBER mailing list
Received on Thu Jul 16 2015 - 06:00:02 PDT
Custom Search