Hi,
the crucial concept here is that Amber will use two end state prmtop
files, V0 and V1 to generate the actual intermediate, lambda-dependent,
states on the fly during the simulation. Your input files will therefore
be the same for all lambda-values (except clambda of course).
> 1. Step 1: removing charge on H6 of BNZ. The input file difference between
> V0 and V1 is the crgmask (except for clambda). What about intermediate
> steps? Should I use the same crgmask as V1, so that AMBER would know what
> atoms are associated with clambda transformation?
each step in that transformation, no matter at what lambda will have the
same crgmask in mdin.V0 and another one in mdin.V1
> 2. Similarly, what are crgmask and scmask supposed to be for the
> intermediate steps with clambda ranging from 0.1 to 0.9? And which prmtop
> file should these substeps be using?
crgmask and scmask define a whole transformation. they will not change
from lambda-window to lambda-window. Likewise, only the end state prmtops
must be supplied.
> 3. For solvation free energy calculation, is one prmtop file enough for
> both
> charge-removing and vdw-removing if softcore potential is applied?
no, a vdw-removing step always implies using two prmtop files.
Effectively, even for a charge-removal step, you use two different
topology/parameter sets but you need not build an extra prmtop and can use
crgmask instead.
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 Tue Mar 15 2011 - 15:00:04 PDT
