Hi,
> I suppose that the restraints (distance/angle) are zero in state 1 and
> are gradually turned on during the first step (1--->2) with maximum/final
> values in state 2
> (these values (force constants) are then used in analyt. calc. of dAr) as
> the whole process (1--->2--->3) should connect two real states. I hope
> this assumption is OK.
that sounds correct.
> So my question is how to do this first step with Amber assuming "One step"
> approach (using simultaneously softcore potentials for vdw and el.
> interactions).
with restraints, I think there is no true *one* step solution yet. You
would activate your restraints first (no softcore required), then
disappear the whole ligand (eel&vdw) while restraints remain in place (no
vacuum step is then required). That's still two steps less than the old
setup :-)
> Restraints for the ligand are defined (in proper RST file) just in case of
> the "V0 system" as the ligand is not present in
> the "V1 system". Am I right ?
yes. That setup comes from Ambers dual topology approach in which V1
doesnt even know that the ligand exists.
> So dvdl_norest=0 or dvdl_norest=1 in this particular case ?
yes, dvdl_norest should only be on when the restraints shall not be
counted, e.g. while disappearing the ligand.
> #lambda 0.1
> Scaling up weight of 20.000 by 1.111
This is done to prevent your restraint force from being scaled down when
you want it to stay in place. The alternative would be to supply a scaled
restraint in V0 at each lambda. Since the restraint only exists in V0, it
will be multiplied by lambda later during the MD, this scaling just
effectively prevents that from happening.
The goal of this is that if you set a 5.0 kcal restraint, sander will
apply that force at any lambda with no adjustment needed by the user. It
is done in this odd way because a restraint is really like an *internal*
potential of the ligand, but it cant be treated like one in the code.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon May 07 2012 - 01:00:03 PDT
