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: [email protected] page:
http://www.trcuyag.blogspot.com___________________________________________________________
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