Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok.
https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 ________________________________ 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 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: > 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. > em.mdp is some corrupted binary file. Please upload a corrected version. -Justin > <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. -- ================================================== 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.
