[gmx-users] Diffusion constant

[Ricardo Cuya Guizado]

Dear Users
I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way:
Obtaining a continuos trajectory
1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc

Obtaining the msd of the solute, removing the center of mass of the system
Firt way:
2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm
I choose SOLUTE

Second way

2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv 
I choose SOLUTE

There are significative differences in the results?
according to the gromacs manual -mv option is used in molecules,

What is the correct step, 2a or 2b?


Regards
Teobaldo

___________________________________________________________Teobaldo Ricardo Cuya Guizado, Msc.Physics DepartmentPontificia Universidade Catolica de Rio de JaneiroRua Marquês de São Vicente, 22522451-900 Gávea - Rio de Janeiro - RJ BRASILPhone: 55-21-7613-3843e-mail: trcuyag at gmail.comWeb page: http://www.trcuyag.blogspot.com___________________________________________________________

 		 	   		  
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