[gmx-users] Re: Re; Force Calculation

Justin M. Shorb shorb at wisc.edu
Thu Jun 29 16:41:17 CEST 2006

Erik and Mark: Thanks for your help, I will begin diving into the code 

Mark, if everything went ideally (which things don't always), I would 
use the force tables to compute the total SR electrostatic force on 
each atom in a specific group (around 2 to 7 atoms). The same goal can 
be accomplished by running a trajectory and then rerunning it to 
calculate the electrostatic forces exclusively. This is what we have 
done before, but saving the necessary trajectory file for our current 
system has gotten too costly. Instead, I am hoping to collect the 
forces and save those exclusively at each timestep (along with 
positions at larger intervals). So far it has seemed that Gromacs 
creates a separate coulombic and LJ table, but uses a combined table to 
actually compute the forces. So it should be capable of computing the 
simple ES force on the fly and saving them. Any suggestions on a better 


More information about the gromacs.org_gmx-users mailing list