Re: [AMBER] free energy calculation with TI

From: Dian Jiao <>
Date: Tue, 15 Mar 2011 21:17:44 -0600

I guess I will need two sets of prm/rst files for vdw-removing simulations.
Take solvation free energy for instance, the prm/rst files for V0 and V1
would be solute+watbox and watbox respectively. According to Amber10 manual,
if softcore is applied, the two prmtop files can have different number of
atoms. However, the common atoms, which are water molecules in this case,
should have identical coordinates. In other words, the two prm/rst files for
V0 and V1 only differ by the solute molecule. Is there a way to generate a
prmtop file by taking out the solute atoms and keep the all other atoms the
same? Or it has to be done manually?

On Tue, Mar 15, 2011 at 4:12 PM, Dian Jiao <> wrote:

> Thanks for the clarification.
> For the vdw-removing step of solvation free energy calculation,
> prmtop/inpcrd files of V0 and V1 are solute+watbox and watbox_only. In
> addition, scmask of V0 should specify all the atoms of the solute. Is that
> correct?
> On Tue, Mar 15, 2011 at 3:31 PM, <> wrote:
>> 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
>> _______________________________________________
>> AMBER mailing list
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Received on Tue Mar 15 2011 - 20:30:05 PDT
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