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

[Justin Lemkul]

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

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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