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.
