Hello Justin, so I believe it's just pbc visualization stuff going on then.. okay.. yes you can do it then from trjconv .
Regards, Debashish On Thu, 7 May 2020, 14:14 Debashish Banerjee, <deb.aerosp...@gmail.com> wrote: > Hello Ekatherina, I did not reach a point in my simulations where I have > used freeze command, but I think for your case, can't you put a position > constraint on your quartz layer. In that case, you just have to create an > index file having quartz in the group and then you can put postion > restraints on them in x,y,z by putting force constant of [1000 1000 1000] > so that the layer doesn't move. > > Regards, > Debashish > > > > > > On Thu, 7 May 2020, 10:28 Ekatherina O, <o...@isc-ras.ru> wrote: > >> Hello Dr. Dallas Warren, >> Thank you for the suggestions. >> >> But this does not solve the problem of the movement of atoms of quartz >> layers (upper and lower) located at the borders of the box. I would like >> the quartz layers to remain intact during the modeling process, i.e. >> atoms did not move and the initial structure was disturbed. How can I >> solve this problem? >> Can I freeze structure (atoms)? Since with a further increase in >> simulation time, I observe the movement of quartz layers in the box. I >> don’t need them to move. >> >> > Message: 4 >> > Date: Tue, 5 May 2020 09:12:51 +1000 >> > From: Dallas Warren <dallas.war...@monash.edu> >> > To: GROMACS users <gmx-us...@gromacs.org> >> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? >> > Message-ID: >> > <CAOv1qzY3iYKVgOTJRb=_ >> dtxkx86ohdbsdyjg2ma2+tpa8ge...@mail.gmail.com> >> > Content-Type: text/plain; charset="UTF-8" >> > >> > 1/ it means that between the original coordinate file loaded with vmd >> > and >> > the frame you are looking at there from the trajectory file, those >> > atoms >> > have moved across the periodic boundary and vmd is still drawing the >> > bond >> > between them. vmd knows nothing about bonds, it guesses where the bonds >> > should be and maintains them between those atoms when viewing a >> > trajectory. >> > If looking to make a nice looking animation simply using gmx trjconv to >> > move the layer into the center of the box. Otherwise use a viewing >> > method >> > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws >> > each frame i.e. DynamicBonds >> > >> > 2/ where the simulation box is located is entirely arbitrary. So if it >> > is >> > not in the location you want then use gmx trjconv to move it to where >> > you >> > want it to be. >> > >> > All these things you are seeing here are artifacts of the periodic >> > boundary >> > condition: >> > >> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc >> > >> > >> > Catch ya, >> > >> > Dr. Dallas Warren >> > Drug Delivery, Disposition and Dynamics >> > Monash Institute of Pharmaceutical Sciences, Monash University >> > 381 Royal Parade, Parkville VIC 3052 >> > dallas.war...@monash.edu >> > --------------------------------- >> > When the only tool you own is a hammer, every problem begins to >> > resemble a >> > nail. >> >> -- >> Yours sincerely, >> Ekatherina O. >> o...@isc-ras.ru >> -- >> 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.