Hi there,
I'm relatively new to AMBER, and I'm interested in running a calculation
that loops over the conformations in a trajectory and prints out the
energies and forces for each conformation. I was able to calculate forces
on a single conformation by running the command: "sander -i force.mdin -o
force.mdout -p res.prmtop -c res.inpcrd" with the following input file:
#==== File Begins ====#
Single Point energy and Force calculation
&cntrl
imin = 0, ntb = 0, cut = 999, nstlim = 0,
/
&debugf
do_debugf = 1, dumpfrc = 1,
/
#==== File Ends ====#
However, when I set imin = 5 and call sander with the extra argument "-y
equilibrate.mdcrd", it still appears to calculate forces for just one
conformation.
Is it possible to calculate forces for each conformation in a trajectory?
If not, then I'll create a series of inpcrd files and call sander multiple
times, although it seems most efficient to do it in a single run.
Thanks,
- Lee-Ping Wang
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Received on Tue May 29 2012 - 00:30:02 PDT
