[gmx-users] regarding editconf

Quyen VuVan vuqv.phys at gmail.com
Mon Jan 21 15:34:36 CET 2019


Hi all,
My point is when you center your solute at (0,0,0) there is a half of your
solute will be placed at the quarter of negative coordinates. And then you
add water, gmx solvate will only add water in positive coordinate region.
Am I right?

On Wed, Jan 16, 2019 at 5:19 AM Omkar Singh <omkantnirala92 at gmail.com>
wrote:

> 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
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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