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

[Benson Muite]

Dear Cheng,
The paper you mentioned (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524983/) uses NAMD (http://www.ks.uiuc.edu/Research/namd/) has somewhat different scalability properties than GROMACS.
Regards,
Benson

On Wed, Apr 8, 2020, at 7:14 AM, ZHANG Cheng wrote:
> 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
> -- 
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