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

[Justin Lemkul]

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

>
>
>
> ------------------ 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

-- 
==================================================

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

==================================================