Dear Cheng, Either fixing or constraining the other units will not decrease the computational cost of the simulation since you will still be computing the interactions between the unit that can move and all the other fixed/constrained units. Andre
On Tue, Apr 7, 2020 at 10:41 AM ZHANG Cheng <272699...@qq.com> wrote: > 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. > -- _____________ 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.
