Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Hello Justin Lemkul, Thank you for the suggestions. I understood and already tried using transforms with trjconv. The picture got better. -- Message: 4 Date: Thu, 7 May 2020 08:17:06 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed On 5/7/20 4:24 AM, Ekatherina O 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? I will reiterate what Dallas has said - if you have atoms that are exactly at the bottom of the box, they effectively *are* the boundary and therefore can seem to "jump" back and forth. This has no implication whatsoever on the physics, just visualization. You can "fix" the issue after the fact with trjconv. 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. Freezing is very artificial and leads to unphysical collisions. Avoid if at all possible. -- 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Hello Debashish, Thank you for the suggestions. Could you tell us in more detail how (in which file) postion restraints on them in x, y, z should be written by putting force constant of [1000 1000 1000 Could you please advise the links where I can read about it? Message: 3 Date: Thu, 7 May 2020 14:14:41 +0200 From: Debashish Banerjee To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset="UTF-8" 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 -- 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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, 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, 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 >> > To: GROMACS users >> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? >> > Message-ID: >> > > 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
On 5/7/20 4:24 AM, Ekatherina O 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? I will reiterate what Dallas has said - if you have atoms that are exactly at the bottom of the box, they effectively *are* the boundary and therefore can seem to "jump" back and forth. This has no implication whatsoever on the physics, just visualization. You can "fix" the issue after the fact with trjconv. 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. Freezing is very artificial and leads to unphysical collisions. Avoid if at all possible. -Justin Message: 4 Date: Tue, 5 May 2020 09:12:51 +1000 From: Dallas Warren To: GROMACS users Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: 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. -- == 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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, 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 > > To: GROMACS users > > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? > > Message-ID: > >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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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 To: GROMACS users Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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. On Mon, 4 May 2020 at 22:08, Ekatherina O wrote: > I have done simulation water in nanopore based on quartz (I use model > ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is > a link to the pictures at the initial time (1.png) and in the modeling > process. > > https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing > ) > Its NVT simulation (see .mdp below) and neutral charge on surface (have > silanol groups), system is overall neutral. > 1) Did I choose the right settings? What do these atomic displacements > (lines in the pictures) mean? What restrictions should be imposed on the > system? > 2) In addition, I noticed that all the atoms of the quartz walls that > are in the vicinity of the box walls move from the upper wall to the > lower and lower to the upper. How can I avoid this when periodic > boundary conditions are imposed? Do I understand correctly that this > involves interaction between the quartz walls? > > integrator = md-vv > dt = 0.001; = 1 fs > nsteps = 50 ; = 100 ps > nstcomm = 1 > ; OUTPUT CONTROL OPTIONS > nstxout = 200 > nstvout = 200 > nstfout = 200 > nstlog = 200 > nstenergy = 200 > energygrps = System > cutoff-scheme= Verlet > ; NEIGHBORSEARCHING PARAMETERS > ;periodic-molecules = no > nstlist = 20 > ns_type = grid > pbc = xyz > rlist = 1.4 > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME ; fourierspacing ; pme-order > ; = PPPM ; fourierspacing > ; = Ewald; No parallel Ewald. > rcoulomb= 1.4 > rvdw= 1.4 > ; Ewald, PME, PPPM options > ;fourierspacing = 0.12 > ;fourier_nx = 0 ; 2 3 5 7 > ;fourier_ny = 0 > ;fourier_nz = 0 > ;pme_order = 6; 10 ; 8 ; default = 4 > optimize_fft= yes > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > Tcoupl = nose-hoover > tc-grps = System > tau_t = 0.5 > ref_t = 298 > ;Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 0.1 > compressibility = 0.0008076 > ref_p = 800 > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp= 298 > gen_seed= 173529 > ; OPTIONS FOR BONDS > constraints = all-bonds > constraint-algorithm = lincs > > > And sorry if I missed similar topic in mailing list, but I couldn't find > anything similar. > > > -- > 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.
[gmx-users] Need help creating md.mdp for silica(quartz)?
I have done simulation water in nanopore based on quartz (I use model ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is a link to the pictures at the initial time (1.png) and in the modeling process. https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing) Its NVT simulation (see .mdp below) and neutral charge on surface (have silanol groups), system is overall neutral. 1) Did I choose the right settings? What do these atomic displacements (lines in the pictures) mean? What restrictions should be imposed on the system? 2) In addition, I noticed that all the atoms of the quartz walls that are in the vicinity of the box walls move from the upper wall to the lower and lower to the upper. How can I avoid this when periodic boundary conditions are imposed? Do I understand correctly that this involves interaction between the quartz walls? integrator = md-vv dt = 0.001; = 1 fs nsteps = 50 ; = 100 ps nstcomm = 1 ; OUTPUT CONTROL OPTIONS nstxout = 200 nstvout = 200 nstfout = 200 nstlog = 200 nstenergy = 200 energygrps = System cutoff-scheme= Verlet ; NEIGHBORSEARCHING PARAMETERS ;periodic-molecules = no nstlist = 20 ns_type = grid pbc = xyz rlist = 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME ; fourierspacing ; pme-order ; = PPPM ; fourierspacing ; = Ewald; No parallel Ewald. rcoulomb= 1.4 rvdw= 1.4 ; Ewald, PME, PPPM options ;fourierspacing = 0.12 ;fourier_nx = 0 ; 2 3 5 7 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 6; 10 ; 8 ; default = 4 optimize_fft= yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = nose-hoover tc-grps = System tau_t = 0.5 ref_t = 298 ;Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.1 compressibility = 0.0008076 ref_p = 800 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp= 298 gen_seed= 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs And sorry if I missed similar topic in mailing list, but I couldn't find anything similar. -- 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.
