[gmx-users] request for enhanced options for force and coord output during mdrun

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jul 14 17:50:59 CEST 2007

I am interested in obtaining forces on particular atoms at each  
integration step. It seems wasteful to use "nstfout = 1" when I only  
want the forces on a couple atoms out of tens of thousands.

My point of interest is this: If I am doing umbrella sampling over a  
spatial coordinate or using dihedral_restraints to generate the PMF  
about a torsion, I am currently limited to data processing by WHAM.  
However, I think that force integration should be more accurate.  I  
can easily subtract the biasing force myself if I save every  
coordinate using xtc_grps since I need to know the position along the  
reaction coordinate anyway in order to properly generate my histogram  

Perhaps it is possible to rig the pull code or the free-energy in  
order to output what I desire without actually doing any  
pulling/switching of lambda values? I looked into the 3.3 manual pages  
35,66,104,119,149 re: free energy code but nothing was immediately  

If not, let me please put in my request for two new .mdp options:
1. "nstfrcout" that defines the number of steps between outputting  
selected forces to a special file = "traj.frc"
2. "force_grps" that controls output selection to the new file = "traj.frc"
* This is intended to have no effect on nstfout.

While I'm at it, the ability to make more than one .xtc file with  
different output selections nstxtcout, xtc_grps, xtc_precision, is  
desirable for example when one wants to save a small group of selected  
coordinates every step for processing and the entire coordinates once  
and a while for later system analysis.

I have added these items to the wiki wish-list

Many thanks,

More information about the gromacs.org_gmx-users mailing list