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.
