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

[André Farias de Moura]

Dear Cheng,

maybe you should step back and begin the planification of your research
project considering how much computer power you have available. If you
cannot handle the whole capsid then you have to simplify the model either
using some coarse grained force field (MARTINI, for instance) or studying a
smaller part of the capsid.

but these choices are up to you, they depend on what questions you are
trying to answer.

Andre


On Wed, Apr 8, 2020 at 12:02 AM ZHANG Cheng <272699575 at qq.com> wrote:

> Dear Justin and Andre,
>
>
> Thank you for the advice. So can I ask how commonly the very large virus
> capsid is simulated? A recent paper "Physical properties of the HIV-1
> capsid from all-atom molecular dynamics simulations" is using 3880 GPU
> accelerated Cray-XK nodes, which is impossible for our university to
> provide.
>
>
>
>
> ------------------&nbsp;Original&nbsp;------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Tue, Apr 7, 2020 10:10 PM
> To:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users at maillist.sys.kth.se&gt;;
>
> Subject:&nbsp;Re:Simulate only one unit of the virus capsid while fixing
> its surrounding units
>
>
>
> 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"?
>
>
> 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.
>
>
>
>
>
> ------------------ Original ------------------
> 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
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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