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

[André Farias de Moura]

Dear Cheng,
Either fixing or constraining the other units will not decrease the
computational cost of the simulation since you will still be computing the
interactions between the unit that can move and all the other
fixed/constrained units.
Andre

On Tue, Apr 7, 2020 at 10:41 AM ZHANG Cheng <272699575 at qq.com> wrote:

> 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