[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
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
nstlist             =  10
ns_type             =  grid
rlist               =  1.0            
;ELECTROSTATIC and VdW parameters.
rcoulomb            =  1.0
rvdw                =  1.0
epsilon-r           =  1           
Tcoupl              =  berendsen
tc-grps		    =  system
tau_t               =  0.1	
ref_t               =  303      
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

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