[gmx-users] Re: g_velacc
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 4 09:39:23 CEST 2013
On 2013-07-04 08:32, Ishwor wrote:
> 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
nstvout = 10
> Thanks
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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