Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations.
<https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: > Hello again, > > I have done a few things since I last updated this list. > > > I generated a new system of only 1000 water instead of the original 2000, I > used a more careful approach in my energy minimization, minimizing first with > all bonds and angles constrained then again without those hash constraints. > This succeeded in getting the maximum force in my system to below 100kcal > without lincs warnings. > > > Then I proceeded to equilibrate the temperature as before with no issues, and > finally I attempted to equilibrate the box size using the Berendsen barostat > running for 2ns. The box size increases as before and still does not > converge. The system stays at around 300K, but after a while (~1ns) it seems > to fill the box like its a gas visually at least. > > So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin > Thanks, > > Andrew > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eisenhart, > Andrew (eisenhaw) <eisen...@mail.uc.edu> > Sent: Thursday, May 31, 2018 1:51:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > Hey, > > Thanks for everyone's response. > > > I have tried using the berendsen barostat, with it I see similar behavior > with the unit cell jumping up in size and then steadily increasing in size. I > have some longer runs using it running now (2-3ns), so I'll be able to see it > it eventually converges. > > > Nice catch with the particle type being incorrect, but with it corrected I'm > still having the same problems (ie the oscillation of the box size) it has > yet to throw lincs warnings though (even at ts = 2fs) so I'm going to > simulate for a longer amount of time to see if it will converge. > > > Thanks again for everyone's reply, below is my .itp in its entirety maybe > there is an error in the exceptions(which im still not 100% sure about) or > something else that will stand out. > > > Andrew > > > ; > > [ atomtypes ] > ; name bond_type mass charge ptype sigma epsilon > qm1 qm1 0.000 -2.516 V 0.000 0.000 > qh1 qh1 0.000 1.258 V 0.000 0.000 > > [ moleculetype ] > ; molname nrexcl > M3 3 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 opls_113 1 M3 OW 1 0.0 > 2 opls_114 1 M3 HW1 1 0.0 > 3 opls_114 1 M3 HW2 1 0.0 > 4 qm1 1 M3 qm 1 -2.516 > 5 qh1 1 M3 qh1 1 1.258 > 6 qh1 1 M3 qh2 1 1.258 > #ifndef FLEXIBLE > > [ settles ] > ; OW funct doh dhh > 1 1 0.09572 0.15139 > #else > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 502416.0 0.09572 502416.0 > 1 3 1 0.09572 502416.0 0.09572 502416.0 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.52 628.02 104.52 628.02 > #endif > > [ exclusions ] > 1 2 3 4 5 6 > 2 1 3 4 5 6 > 3 1 2 4 5 6 > 4 1 2 3 5 6 > 5 1 2 3 4 6 > 6 1 2 3 4 5 > > [ virtual_sites3 ] > ; Vsite from funct a b > 4 1 2 3 1 0.29869481802 0.29869481802 > ; Vsite (3fad) funct theta d > 5 3 2 1 3 18.06 0.025 > 6 2 3 1 3 18.06 0.025 > > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham > <mark.j.abra...@gmail.com> > Sent: Thursday, May 31, 2018 7:54:09 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > Hi, > > If that fixes the issue, then please let us know - we should consider > fixing grompp to check that the inputs have appropriate consistency. > > Mark > > On Thu, May 31, 2018 at 1:48 PM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: >>> Hello all, >>> >>> I am having an issue with the current systems I am working on. The >> system consists of 2000 6point water molecules (3 chargeless masses for Ow, >> hw1, and hw2; and 3 massless point charges for the electrostatics). The >> three point charges I have implemented as virtual interaction sites using >> the section below in my topology file. >>> >>> [ virtual_sites3 ] >>> ; Vsite from funct a b >>> 4 1 2 3 1 0.29869481802 0.29869481802 >>> ; Vsite (3fad) funct theta d >>> 5 3 2 1 3 18.06 0.025 >>> 6 2 3 1 3 18.06 0.025 >>> >>> >>> this is loosely based on the tip4p model. Since the two partial charges >> off of the hydrogens differ only in location I have them defined as a >> single type with sigma and epsilon defined as 0. I have also done this to >> the partial charge off of the oxygen. This is all seen below in my >> atomtypes and atoms sections. >>> >>> [ atomtypes ] >>> ; name bond_type mass charge ptype sigma epsilon >>> qm1 qm1 0.000 -2.516 A 0.000 0.000 >>> qh1 qh1 0.000 1.258 A 0.000 0.000 >> The particle type for these should be V. This could be the problem - if >> you've encoded an incorrect particle type then the update routines will >> not propagate them correctly. >> >> -Justin >> >>> ----------------------------------- >>> >>> [ atoms ] >>> ; id at type res nr residu name at name cg nr charge >>> 1 opls_113 1 M3 OW 1 0.0 >>> 2 opls_114 1 M3 HW1 1 0.0 >>> 3 opls_114 1 M3 HW2 1 0.0 >>> 4 qm1 1 M3 qm 1 -2.516 >>> 5 qh1 1 M3 qh1 1 1.258 >>> 6 qh1 1 M3 qh2 1 1.258 >>> >>> The problem I am seeing right now depends on the parameters I use in the >> mdp files. During thermostat equlibration nothing is amiss, but once the >> volume of the box is allowed to relax the problems show. Using the >> parrinello-rahman barostat and 0.002fs timestep I crash with lincs >> warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but >> the box size never converges It instead expands to around 10x its original >> size. So I think that I must have a problem with the implementation of my >> virtual sites. Any guidance would be greatly appreciated. Thanks below are >> some other parameters I have set in my input files. >>> Andrew >>> >>> >>> integrator = md >>> nsteps = 500000 >>> nstcomm = 100 >>> nstxout = 0 >>> nstvout = 0 >>> nstfout = 0 >>> nstlog = 1000 >>> nstenergy = 1000 >>> nstxtcout = 1000 >>> nstlist = 5 >>> ns_type = grid >>> pbc = xyz >>> coulombtype = pme >>> rcoulomb = 0.5 >>> rlist = 0.5 >>> vdw-type = cut-off >>> rvdw =0.5 >>> constraint_algorithm = lincs >>> constraints = all-bonds >>> lincs_iter = 1 >>> lincs_order = 8 >>> fourierspacing = 0.10 >>> pme_order = 6 >>> ewald_rtol = 1e-06 >>> ewald_geometry = 3d >>> optimize_fft = yes >>> tcoupl = Nose-Hoover >>> tc-grps = System >>> tau_t = 0.4 >>> ref_t = 300 >>> ; Pressure coupling is on >>> pcoupl = parrinello-rahman >>> pcoupltype = isotropic >>> tau_p = 2.0 >>> ref_p = 1.0 >>> compressibility = 4.5e-5 >>> refcoord-scaling = com >>> DispCorr = EnerPres >>> comm-mode = linear >>> >>> >>> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 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. >> > -- > 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. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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. -- 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.
