Hello Gromacs users, I've been trying to run a system of benzene at 298 K and 1 bar as a test for future use as a solvent and have built it in OPLS using opls_145 for the carbons and opls_146 for the hydrogens, these are listed in the ffoplsaa files as benzene parameters. However I've found that over a reletively short run the system is apparently freezing into a solid (density goes to 1000 when it should be around 800) but both the temperature and pressure look like what I'm coupling to.
I'm not sure if I've made a huge error in something or what is going on, I'll include my itp file here: [ moleculetype ] Ben 3 [ atoms ] 1 opls_145 1 Ben C 1 -0.115 12.011 2 opls_145 1 Ben C 2 -0.115 12.011 3 opls_145 1 Ben C 3 -0.115 12.011 4 opls_145 1 Ben C 4 -0.115 12.011 5 opls_145 1 Ben C 5 -0.115 12.011 6 opls_145 1 Ben C 6 -0.115 12.011 7 opls_146 1 Ben H 1 0.115 1.00800 8 opls_146 1 Ben H 2 0.115 1.00800 9 opls_146 1 Ben H 3 0.115 1.00800 10 opls_146 1 Ben H 4 0.115 1.00800 11 opls_146 1 Ben H 5 0.115 1.00800 12 opls_146 1 Ben H 6 0.115 1.00800 [ bonds ] 1 2 1 1 6 1 1 7 1 2 3 1 2 8 1 3 4 1 3 9 1 4 5 1 4 10 1 5 6 1 5 11 1 6 12 1 [ angles ] 1 2 3 1 1 2 8 1 1 6 5 1 1 6 12 1 2 1 6 1 2 1 7 1 2 3 4 1 2 3 9 1 3 2 8 1 3 4 5 1 3 4 10 1 4 3 9 1 4 5 6 1 4 5 11 1 5 4 10 1 5 6 12 1 6 1 7 1 6 5 11 1 [ dihedrals ] 1 2 3 4 3 1 2 3 9 3 1 6 5 4 3 1 6 5 11 3 2 1 6 5 3 2 1 6 12 3 2 3 4 5 3 2 3 4 10 3 3 2 1 6 3 3 2 1 7 3 3 4 5 6 3 3 4 5 11 3 4 3 2 8 3 4 5 6 12 3 5 4 3 9 3 5 6 1 7 3 6 1 2 8 3 6 5 4 10 3 7 1 2 8 3 7 1 6 12 3 8 2 3 9 3 9 3 4 10 3 10 4 5 11 3 11 5 6 12 3 and my mdp file(edited out some comments that aren't important): nsteps = 200000 ; Output frequency for xtc file = nstxtcout = 500 ;Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 500 nstvout = 500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstenergy = 500 energy_grps = Ben ; Temperature(K) & Pressure(bar) gen_temp = 298.15 ref_t = 298.15 comm_mode = None ;Not all things will use xtc output, but if we define it here, ;then the other files should never need changing. xtc_grps = Ben coulombtype = Cut-off ;Pressure (in units: bar) ref_p = 1 ;;;OUTPUT;;; ;Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 0 nstenergy = 50000 ;;;TEMPERATURE;;; ;generation is disabled, but gen_temp must be set for files importing this one gen_vel = yes gen_seed = -1 tau_t = 0.1 Tcoupl = Berendsen tc-grps = System ;;;PRESSURE;;; Pcoupl = Berendsen tau_p = 0.1 compressibility = 4.5e-5 ; These are all = 1 by default, so they could possibly be left out rlist = 1.5 rcoulomb = 1.5 rvdw = 1.5 vdwtype = Cut-off coulombtype = Cut-off ; Output frequency for all pair energies (can make LARGE files) (0=never) nstdisreout = 0 ; Apply long range dispersion corrections for Energy and Pressure ; We might not want this at all, default is = no DispCorr = EnerPres ;steps between neighbor list updates = nstlist = 5 ;Something to do with energy minimization...? emtol = 100 ; Non-equilibrium MD stuff ;freezegrps = ;freezedim = ;energygrp_excl: = DRG DRG ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble ;disre = No ;disre = Simple ; Force weighting of pairs in one distance restraint: Conservative or Equal ;disre-weighting = Conservative disre-weighting = Equal ; Use sqrt of the time averaged times the instantaneous violation ;disre-mixed = no ;disre-fc = 1000 ;disre-tau = 0 ; Output frequency for pair distances to energy file I've tried several things including pressurizing to 1000 bar then releasing it to 1 bar and have had no success. Any suggestions would be much appreciated, Jeffery Perkins -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
