AMBER Archive (2009)

Subject: Re: [AMBER] Partial interactions

Date: Fri Apr 24 2009 - 11:20:21 CDT

Hi Ignacio,

> If you don't mind, I still have a couple of questions, now on the
> application part: I need to calculate the free energy of some small system
> when it dissapears. I have started to do this in the following way:
> a) Use ifsc=1, defining V0 as the entire system and V1 as only one atom of
> the original ones (so that I don't have an empty prmtop file which I think
> Amber can't handle).
> b) After starting doing 1), I read something about using ifsc=2, another
> approach to make a system dissapear.

Im not sure what you really want to do there. The free energy of
disappearing a complete system in vacuum is zero, because there is nothing
it disappears from, i.e. no change in the Hamiltonian. The only exception
to this is that in the implementation as it is now, removing all charges
from a system in vacuum also removes its internal 1-4 EEL interactions
which needs to be corrected for (See the Steinbrecher et al. 2007 JCP
paper for an explanation). ifsc=2 is a legacy option from an earlier
implementation that allows you to completely remove a system (i.e. it
implicitly assumes the empty prmtop at V1 that, as you correctly state,
Amber cant handle). The way the implementation is now, ifsc=2 should not
be necessary in any meaningful setup.

One way softcore TI should be setup is described in:

> 1) From the implementation point of view, are both approaches equivalent?
> 2) In approach a), and as it is usualy done, I first make the charges
> dissapear, and in a second step I use softcore potentials. In this second
> step, Sander complaints if I try to use what sounds reasonable to me,
> ifsc=1
> for V0 (the dissapearing system) and ifsc=0 for V1 (where nothing appear
> nor
> dissapear). So I imagine I just have to set ifsc=1 on both, even when V1
> doesn't really use soft core potentials. Is this right?

If you set ifsc=1 you must do so in both input files, because both
processes need to know that there may be different numbers of atoms in the
partner process so they need to use different routines to mix the forces
etc. Even with ifsc=1 only the atoms in scmask (which may very well be an
emtpy string) will experience the SC potential.



Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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