Hi Samuel,
> (nmropt=1) to the benzene molecule. To perturb to nothing I use the
> option ifsc=2, as explained in the manual. But when I run sander it
> stucks at a particular place in the initialization phase. I have tried
I can't comment much on the energy decomposition you want to use, but to
conduct the TI calculation you describe, you would not use ifsc=2. This is
a special case that only concerns perturbing the complete system to
nothing, which can then no longer run in parallel, since you have no
second prmtop file. A protein+benzene -> protein perturbation would still
run with ifsc=1.
ifsc=2 implies a serial run, this may very well be the cause auf the
hangup you see, since TI decomp assumes you run a multisander-job with two
groups.
> to set ifsc to 0, and then sander runs perfectly fine. By looking
It's suprising that you can run this with ifsc=0, because your two systems
would have different numbers of atoms and that would cause a TI
calculation to crash without the soft core options to handle extra atoms.
Looking at your input file:
> icfe=0, clambda=0.90,
This would not be a TI run at all if you set ifsc=0. You have to set
icfe=1 if you want to use TI, only in the special case of ifsc=2, which
doesnt apply here, can you run a TI-like calculation without icfe>0.
I guess the documentation could be clearer about ifsc=2, which has become
more of a legacy option, since the internal energies are now not scaled by
lambda, so perturbing a complete system to nothing should always give you
dVdl=0. The option may even disappear from future versions of Amber...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 13 2010 - 03:00:03 PST
