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 -- 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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists