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: "ZHANG Cheng"<272699...@qq.com>; > Date: Wed, Apr 8, 2020 11:02 AM > To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; > > Subject: 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: "ZHANG Cheng"<272699...@qq.com>; > Date: Tue, Apr 7, 2020 10:10 PM > To: "ZHANG > Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; > > Subject: 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: "ZHANG Cheng"<272699...@qq.com>; > Date: Tue, Apr 7, 2020 09:41 PM > To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; > Cc: "ZHANG Cheng"<272699...@qq.com>; > Subject: 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
