From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] soft-core potential in combination with PME
(sorry,again)
Date: Fri, 13 Apr 2007 09:18:21 -0700
Berk and all,
I don't understand what David Mobley meant exactly.
There is no Coulomb singularity with soft-core.
Maybe one could have an unfortunate situation where the LJ
is already very soft, but the Coulomb not very soft,
which could lead to instabilities.
But I have never encountered this.
Anytime I do a simulation where I turn of both coulomb and LJ
interactions at the same time, I run into this problem. Sometimes it's
worse than others. Maybe it's because the 1/r^12 and 1/r have
different r-dependencies? I don't know.
I suspect the issue partly is just what's optimal: The soft core
parameters that would be optimal for modifying Coulomb interactions
are not optimal for modifying LJ interactions, and vise versa. So if
you use soft core settings that give you a smooth transformation for
LJ interactions, you do too much or too little smoothing of the
Coulomb interactions and introduce large Coulombic forces. On the
other hand, if you pick soft core parameters that are good for Coulomb
interactions, you end up with large LJ forces. (For example, Coulomb
transformations are nearly optimal with LINEAR lambda scaling
(sc-alpha=0), but that doesn't work *at all* for LJ transformations.
If I remember correctly, basically what the Anwar paper tries to
achieve is separately smoothing the two. You could probably accomplish
the same thing by allowing separate sc-alpha and sc-power for Coulomb
and LJ interactions so they can be tuned separately.
So, while formally using soft core for Coulomb removes the
singularity, in practice I think the forces are still large enough
(when using soft core parameters are tuned for LJ interactions) that
instabilities result (at least for the stuff I do, with the force
field I use). Hence my recommendation to do two stages.
Anecdotally, I should mention that a bunch of different people have
e-mailed asking me about various problems they're having where they
get unexpected free energies, etc. I suggest they do the Coulombic and
LJ parts separately, and invariably they write back that it works much
better.
David
I agree that doing it separately is more efficient and causes less trouble.
That would also be my advice.
I can only say that I have never encountered instabilities,
although I have had systems where I needed a lot of sampling
because of inconvenient Coulomb vs LJ soft-core paths.
I have not read Anwar's paper, but I think it would be impossible
to devise a different Coulomb and LJ scaling that would solve
the problem, as you also have to deal with neighboring atoms.
The main problem is usually in hydrogen bonds involving hydrogens bound
to other atoms.
Berk.
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