[gmx-users] OPLS benzene issue
David van der Spoel
spoel at xray.bmc.uu.se
Mon May 10 21:55:18 CEST 2010
On 5/10/10 9:29 PM, Jeffery Perkins wrote:
> 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:
>
You should change the out of plane dihedrals to type 1 (for the H). How
about constraints, do you use them? And the time step? Have you checked
temperature and energies?
> [ 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
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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