AMBER Archive (2009)

Subject: Re: [AMBER] Partial interactions

From: Ignacio J. General (
Date: Fri Apr 24 2009 - 12:11:31 CDT

Hi Thomas. Sorry for the confusion; let me put it in this way:
What I want is to make some system disappear, and calculate the free energy
associated with that process. By that, I mean the energy necessary to
deconstruct, block by block, the original system (of course, there is
something strange here that I am ignoring by the moment, because I am
assuming the system is in an ensemble with constant temperature, but what's
temperature when you only have a few atoms...). So, in this sense, the free
energy to make it disappear is not zero.

In terms of the TI integral equation, what I want is the integral from 0
(whole system) to 1 (only a couple of atoms) of <dv/dl>, where lambda (in
some form) is applied to every interaction of the original system, so that
the system is effectively deconstructed.

So, the question is: if I set up V0 as the whole system and V1 as a couple
of atoms (from the original ones) and use ifsc=1, will sander give the dv/dl
corresponding to what's above?

Thanks again,


On Fri, Apr 24, 2009 at 12:20 PM, <> wrote:

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