[gmx-users] regarding editconf

Omkar Singh omkantnirala92 at gmail.com
Wed Jan 16 05:19:01 CET 2019


My advice is that don't use many option in on shot. In place of -center try
by -translate with rotation.

Best regard

On Tue, Jan 15, 2019 at 8:52 PM Ali Khodayari <
ali.khodayari at student.kuleuven.be> wrote:

> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
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> Virginia Tech Department of Biochemistry
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> http://www.thelemkullab.com
>
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