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
bins.
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
apparent.
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
http://wiki.gromacs.org/index.php?title=Category:Development&action=submit#Wish_list
Many thanks,
Chris.
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