[gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

[André Farias de Moura]

Dear Cheng,

I also think that freezing introduces more artifacts than benefits, since
you are probably beginning your simulation from a crystallographic
structure and fixing most of the molecules will provide a crystal-like
structure, not a relaxed structure closer to the typical physiological
conditions.

Andre

On Tue, Apr 7, 2020 at 11:29 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/7/20 10:10 AM, ZHANG Cheng wrote:
> > Dear Andre, Thank you for the advice. Can I ask,
> >
> >
> > 1) Could you please clarify the concepts? I know "constraint" and
> "restraint" are two different things in gromacs. And "fix" is another term?
> How about "freezegrps"?
>
> I would not use "fix" and "restrain" interchangeably. Fixing a quantity
> means it cannot vary. With a restraint, movement is disfavored but not
> prevented. Freezing is totally artificial and requires you to ignore
> nonbonded interactions between the frozen groups.
>
> >
> > 2) It is okay that the computational time is not reduced, as now only
> several proteins are simulated. If I simulate all the several protein
> without any fixing, I worry they will lose their conformation. So fixing
> the neighbours and only focusing on the protein in the centre could be the
> solution.
> >
>
> Your approach assumes that the conformations of the proteins are not
> dependent on their neighbors. I do not think that is a justifiable
> assumption. If you simulate one protein freely and restrain its
> neighbors, you're doing a glorified simulation of a crystal, which is
> not reflective of biological reality for a virus capsid.
>
> -Justin
>
> >
> >
> >
> > ------------------&nbsp;Original&nbsp;------------------
> > From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> > Date:&nbsp;Tue, Apr 7, 2020 09:41 PM
> > To:&nbsp;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
> > Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> > Subject:&nbsp;Simulate only one unit of the virus capsid while fixing
> its surrounding units
> >
> >
> >
> > It is a challenge to simulate the entire virus as it is too big and I do
> not have such computational resources. So I was thinking to only simulate
> one coat protein and its surrounding neighbours, but keep the neighbours
> relatively fixed.
> >
> >
> > Can I ask
> >
> >
> > 1) Is this a sensible idea to proceed?
> >
> >
> > 2) To fix the neighbours, should I use "constraints" or "restraints"?
> >
> >
> > 3) At which step should I start to introduce the fixation?
> >
> >
> > 4) If possible, is there a tutorial for this? I feel the information
> here is still not straightforward to follow
> > http://www.gromacs.org/Documentation/How-tos/Position_Restraints
> >
> >
> > Thank you!
> >
> >
> > Yours sincerely
> > Cheng
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
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>
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090