Dear Cheng, I also think that freezing introduces more artifacts than benefits, since you are probably beginning your simulation from a crystallographic structure and fixing most of the molecules will provide a crystal-like structure, not a relaxed structure closer to the typical physiological conditions.
Andre On Tue, Apr 7, 2020 at 11:29 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > 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: "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 > > -- > ================================================== > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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.