Hi,
> the calculation again activating the DVDL energy decompostion to check the
> breakdown.
The calculations you already did should have a dvdl breakdown at the end
of mdout, idecomp just breaks it down further by residue etc IIRC.
> 1) According to the amber manual, the "idecomp" options to switch on the
> DVDL breakdown are "=1" and "=2". The first option adds the 1-4 non bonded
> energies to the internal energies, and the second option to the EEL and
> VDW. In my particular case, it seems that the best option would be
> selecting "idecomp=2" (not sure anyway). Actually, I'm wondering in what
> situations is better so select option 1 or 2. Could you please give any
> advice/reference about this?
I would consider 1-4 interactions to be internal energies, so I dont see
when option 2 would be useful. Anyway, no matter how you decompose them,
the huge energies from individual substeps of a TI calculation can not be
interpreted in a meaningful way. However, you can rationalize them in
terms of what contributions in the force field they come from.
> 2) At the beginning I was running my tests in two different ways: In the
> first one, I switched off/on ALL the charges in the glucose molecule, and
...
> really non-negligible. So, do you think it is better to switch off/on all
> the charges in the molecule as I do rather
> than only the charges in the mutated atoms as in the tutorial?
Other people may have different opinions here, but I believe that running
with non-zero or even fractional charges is not a problem per se in MD.
For TI it is almost unavoidable. So I would not worry about net charge and
instead keep the perturbation as small as possible, so change only these
charges that have to change. For Glucose, you are effectively making it a
very nonpolar molecule and then repolarize it by removing/adding all
charges, which seems an inefficient way to change a small part of the
molecule.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Jan 28 2013 - 05:30:03 PST
