[gmx-users] Re: g_velacc

[Dr. Vitaly Chaban]

It would be nice to see plotted velocity autocorrelation function, VACF,
which you integrate?

The resulting diffusion constant looks crazy large, so there must be
something rotten in the VACF.



Dr. Vitaly V. Chaban


On Thu, Jul 4, 2013 at 8:32 AM, Ishwor <ishwor.poudyal19 at gmail.com> 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
> Thanks
>
>
>
>
> --
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