[gmx-users] Re: g_velacc

[David van der Spoel]

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