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

[ZHANG Cheng]

Dear Andre,


Thank you. We are trying to use an adenovirus as a vaccine. As it is not stable, we want to simulate it to identify the unstable regions (e.g. flexible), so as to either engineering (e.g. mutation) it, or adding excipients. 


Simulating only one protein of the capsid is of course doable. But do you think simulating one protein without its neighbours could reflect its dynamics? Would its boundary residues behave very differently compared to with neighbours?
------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Wed, Apr 8, 2020 11:02 AM
To:&nbsp;"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 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.




------------------ Original ------------------
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