Respectable Justin/David/Mark
I used ffgmx force field thinking it as suitable for bonds in the oxygen
molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which
matches with that given in the gromacs manual. After equilibrating my system of
1 oxygen and 255 water molecules in NPT ensemble at 1 bar and 298 K i subjected
it to the NVT ensemble for about 50 ns. The msd is not a straight line. It
increases linearly for first 20 ns and after some ns it decreases linearly
giving negative diffusion coefficient. Could you help me out with it? The model
contains L-J interaction between oxygen and water molecule. The mdp file used
for production run is as follows:
;RUN CONTROL parameters.
integrator = md
dt = 0.002 ; ps !
nsteps = 50000000 ; total 1 ns.
nstcomm = 1
;LANGEVIN DYNAMICS parameters have not been specified as the integrator is
;md
;OUPUT CONTROL parameters.
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
energygrps = OMOL SOL
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 0.9 ;initially 1 I modified to 0.9
;ELECTROSTATIC and VdW parameters.
rcoulomb = 0.9
rvdw = 0.9
epsilon-r = 1
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = berendsen
tc-grps = OMOL SOL
tau_t = 0.001 0.01
ref_t = 298 298
;PRESSURE COUPLING is on
Pcoupl = no;berendsen; berendsen exponential relaxation coupling
tau_p = 0.1;modified from 0.5
compressibility = 4.6e-5
ref_p = 1.0
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 298 K.
gen_vel = no; ; generate initially
gen_temp = 298
gen_seed = 173529 ;give different values for different trials.
;BONDS parameters
constraints = all-bonds
constraint-algorithm = shake
unconstrained-start = yes
and the msd curve is attached in the next mail due to insufficient space
Your help is necessary for me.
Sunil Kumar Thapa
Tribhuvan University, Nepal
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