GMX Users:
When I run grompp on methanol in water in v. 4.5.3 I get the following Note:
NOTE 1 [file methanol.top, line 73]:
The bond in molecule-type MET between atoms 5 OA and 6 HO has an
estimated oscillational period of 9.0e-03 ps, which is less than 10 times
the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Here is my mdp file:
; User Robin
; Wed Dec.1 2010
; Input file
;
title = Yo
cpp = /lib/cpp
integrator = md
dt = 0.001 ; ps !
nsteps = 1100000 ; total 1000 ps=1 ns
nstcomm = 10
; (x) coordinates, (v) is velocities, (f) is forces
; This affects "traj.trr"
; these numbers shouldn't be too small (100,000), takes up disk space
nstxout = 1000
nstvout = 1000
nstfout = 1000
; Output frequency for energies
nstlog = 100
nstenergy = 100
; This affects ".xtc" file for movies this should be a fairly small number
nstxtcout = 100
xtc-precision = 1000
; parameters for neighbors
nstlist = 10
ns_type = grid
rlist = 0.9
; electrostatics
coulombtype = pme
pme_order = 4
ewald_rtol = 1e-5
ewald_geometry = 3d
epsilon_surface = 0
fourierspacing = 0.1
fourier_nx = 0.0
fourier_ny = 0.0
fourier_nz = 0.0
rcoulomb = 0.9
optimize_fft = yes
Dispcorr = EnerPres
vdwtype = cutoff
rvdw_switch = 0.85
rvdw = 0.9
; Berendsen temperature coupling is on in two groups
Tcoupl = v_rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
; Energy monitoring
energygrps = MET SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
Here is my top file:
;
;
; Include forcefield parameters
#include "ffoplsaa.itp"
;
; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
;
[ moleculetype ]
; name nrexcl
MET 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 opls_157 1 MET C 1 0.145
2 opls_156 1 MET H 1 0.04
3 opls_156 1 MET H 1 0.04
4 opls_156 1 MET H 1 0.04
5 opls_154 1 MET OA 1 -0.683
6 opls_155 1 MET HO 1 0.418
[ bonds ]
; ai aj funct c0 c1
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
[ pairs ]
; i j funct
2 6
3 6
4 6
[ angles ]
; ai aj ak funct c0 c1
; H3
2 1 5 1
3 1 5 1
4 1 5 1
4 1 3 1
4 1 2 1
[ system ]
; Name
MET in water
[ molecules ]
; Compound #mols
MET 1
SOL 503
Do I need to add some sort of constraint on my methanol molecule?
Thanks,
Robin
--
Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907
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