[gmx-users] regarding editconf

[Justin Lemkul]

On 1/15/19 9:34 AM, Ali Khodayari wrote:
> Thank you for your response Justin!
> I don't really see how it can cause an error, while it might be just a
> visualization defect in VMD.
> Previously, I tried to perform each step separately, like doing a centering
> by -center 0 0 0, but even performing this step leads to the error "step 0:
> Water molecule starting at atom 40225 can not be settled." The only
> difference would be a change in the coordinates, no? It is not due to the
> fact that I am using 5.1.2 version, is it?

Systems can become unstable for any number of reasons, but not simply 
because some part of a protein appears to be protruding into space. 
That's just normal PBC.

5.1.2 is very old but I don't know of any specific reason why it should 
cause a problem.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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