Hello Jason,
yeah, ok. That is a very good point with the infinite acceleration.
Haven't thought of that. The kinetics was my concern, but as you pointed
out, it does not matter for the equilibrium properties. Ok.
As for why I am doing this, that's a little tricky to explain :)
Basically, I have a protein in explicit solvent and I am mutating some
of its charged residues (Lys, Asp, etc.) into various different amino
acids, most of them uncharged.
This obviously changes the net charge of the system away from
neutrality... so I figured that I could keep it the same by
simultaneously transforming one of the explicit ions (either cations or
anions) into a chargeless dummy particle.
The approach with dummy particle is a little clumsy, but I haven't
figured out a way to simultaneously transform one amino acid with SC
while also decoupling an ion from the system...
Best regards,
Miroslav Krepl
On Sun, 2014-10-05 at 21:02 -0400, Jason Swails wrote:
> On Oct 5, 2014, at 4:11 PM, Miroslav Krepl <krepl.seznam.cz> wrote:
>
> > Dear Amber users,
> >
> > by any chance, did any of you eventually figure out a solution to this
> > problem:
> >
> > http://archive.ambermd.org/201208/0452.html
> >
> > ?
> >
> > I can confirm that two years later, the pmemd.MPI in amber 14 is still
> > doing the same thing for my dummy atoms, i.e. reporting message
> >
> > "ERROR: PMEMD does not support single H residues! “
> >
> > for my dummy atom and then crushing down...
> >
> > I have been using transformation into dummy atoms in the newly
> > implemented one-topology Thermodynamic integration in pmemd.
> >
> > ---
> >
> > I think that I managed to identify the cause of the problem...
> >
> > I tried changing different parameters of the dummy atoms using parmed.py
> > and I eventually figured out that the zero atomic mass is somehow
> > offending the pmemd...
> >
> > It seems that pmemd thinks all atoms with smaller mass than hydrogen
> > (e.g. the zero-mass dummy atoms) are hydrogen!!!!
> >
> > I tried setting the dummy mass to "0"... simulation crushed with the
> > message.
>
> You can’t integrate atoms with a mass of 0. Consider Newton’s equation — F=ma. If the force is non-zero, the acceleration is infinite. It’s not at all unusual that an MD code doesn’t handle atoms with a mass of 0 (virtual sites are different beasts altogether).
>
> > I tried setting the dummy mass to "1"... simulation crushed with the
> > message.
> >
> > I tried setting the dummy mass to "2"... simulation run completely fine
> > (albeit obviously generating wrong results because the dummy atom now
> > has non-zero mass).
>
> Define “wrong results”. Equilibrium properties are independent of mass. It messes up the kinetics (how much depends on how “wrong” the masses are). To my knowledge, dummy atoms have usually been given the mass of the atoms they are “replacing”. But read on below…
>
> > ---
> >
> > Unless I am missing something else, I'd like to report this behavior
> > (identifying atoms with lower mass than hydrogen as hydrogens) as
> > possible bug of the pmemd.
> >
> > Right now it is limiting the applicability of the new TI implementation
> > (which is pretty great otherwise).
>
> I’m curious as to why you think that you require dummy atoms for softcore TI. They shouldn’t be necessary for either pmemd or sander (only if you do not use softcore in sander should they be necessary).
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Mon Oct 06 2014 - 01:30:02 PDT
