[gmx-users] regarding editconf

[Ali Khodayari]

Thank you Justin. I try to search more for the reason. My best, Ali

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Lemkul
Sent: dinsdag 15 januari 2019 16:10
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] regarding editconf



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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