[gmx-users] Re: g_velacc
Ishwor
ishwor.poudyal19 at gmail.com
Thu Jul 4 08:32:02 CEST 2013
I have really tried to calculate diffusion coefficient using both commands
but i cant find the comparable results.
i have my *.mdp file as
;PREPROCESSING parameters
tinit = 0
integrator = md
dt =.002
nsteps = 100000000
nstcomm = 1
;OUPUT CONTROL parameters.
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
nstxtcout = 500
energygrps = system
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 1.0
;ELECTROSTATIC and VdW parameters.
rcoulomb = 1.0
rvdw = 1.0
epsilon-r = 1
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = berendsen
tc-grps = system
tau_t = 0.1
ref_t = 303
;PRESSURE COUPLING is on
Pcoupl = no
gen_vel = no;
;BONDS parameters
constraints = all-bonds
constraint-algorithm = shake
unconstrained-start = yes
pbc = xyz
i have calculated the diffusion coefficient using Einsteins law and found
2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve.
To calculate the diffusion coefficient using g_velacc i used the command
g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen
2001 -mol
and integrate using g_analyze -f vac.xvg -integrate
but i found the result
Calculating the integral using the trapezium rule
Integral 1 0.11915 +/- 0.00000
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233
I guess the required integral value is 0.11915 and to find diffusion
coefficient i divide the result by 3 but get the result not matching with
the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps.
I dont know whether i am in the correct path or there is some problems with
my doings.
i am waiting for the suggestions
Thanks
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