[gmx-users] gmx velacc

[Gregory Poon]

Hello to everyone:

I am trying to use velacc to compute the diffusion constant of a 
globular protein that I have simulated for 100 ns.  I am having a hard 
time figuring out how to have the index.ndx file "the index group 
consist of molecule numbers instead of atom numbers."  What exactly are 
"molecule numbers"?  I have tried to google and looked at previous posts 
on the mailing list to no avail.

Thanks in advance,

Gregory