Fw: [gmx-users] water molecule can not be settled

Justin Lemkul jalemkul at vt.edu
Fri Apr 5 17:12:00 CEST 2013

On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> I' d like to know if it is acceptable to change the molecule coordinates
> to solve this problem?
It's unlikely that some ad hoc change will magically fix a problem.  Energy
minimization should take care of clashes.

> Some time back, I deleted such a molecule and then I got a fatal error
> containing that the trj file and other inputs are not inconsistent.
Right, because you've now changed the contents of the system.  It no longer
matches the topology and the trajectory would then be discontinuous.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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