[gmx-users] RE: Diffusion constant

[Ricardo Cuya Guizado]

Dears Justin and Vitaly

I make a mistake in my firts e-mail

the option is not -mv is -mol as Justin mentioned

So the second step was:

Obtaining the msd of the solute, removing the center of mass of thesystem
Firts way:2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcommI choose SOLUTESecond way 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mol I choose SOLUTE In the two cases the solute was choose , the differences in the solute Cont. Diffusion is in one order of magnitude. What is the correct step for calculate the Dif. const , 2a or 2b?

Regars

Ricardo 		 	   		  
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