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
sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel
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