[gmx-users] g_velacc

rams rams rams.crux at gmail.com
Fri Aug 29 23:32:15 CEST 2008

Dear Users,

I am trying to calculate the velocity correlation functions to estimate the
diffusion constant of my protein which is having nearly 50 residues. I am
using the following command:

g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp

the output is the following:

COR: Correlation time (plain integral from  0.000 to 2500.000 ps) =  0.90300
COR: Relaxation times are computed as fit to an exponential:
COR:   y = exp(-x/a1)
COR: Fit to correlation function from  0.000 ps to 2500.000 ps, results in a
COR:   Fit from   Integral Tail Value   Sum (ps)    a1
COR: 0.0000e+00 0.0000e+00 1.0458e-01 1.0458e-01  1.0458e-01

I have no idea about the output to understand. I understood it is trying to
fit to the equation it displayed but have no idea about the number 0.90300

The .xvg plot I got is so surprising its just a straight line parallel to
time axis. I am sure I am making some mistake as I am using g_velacc for the
first time.

>From this if we want  to get the Diffusion coefficient we need to integrate
the correlation time from 0 to infinitive as it is described in the manual.
Is there any way we can do it by using any of the options or we need to do
it separately by using any other tools ? If so please let me know.

I also wanted to know the following things:

What does the following options do:

-integrate (in g_analyze)

-fitfn (there are couple of options are given if any one have idea about the
sources for them ?)

I calculated the diffusion coefficients using g_msd also, it gave the
diffusion coefficient value as 6.0*10^-6. Which is quite large compared to
the values reported in the literature which are around 2.0*10^-6. Whats
going wrong here also it is not generating the output .xvg file. (It is
complaining input/output fatal error).

Thanks in advance,
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