Hi Fiske,
From what I understand, you want to compute the free energy for
changing one or more atoms in the QM subsystem. I never considered doing
this because I do not expect to get sufficient sampling. But in my
opinion this should be possible.
In case only atoms in the QM subsystem change it is straightforward. But
I might overlook something important (maybe someone can comment on this
if I make a mistake).
I think you should modify the code, so that there are two QM/MM
computations per step. Once in the A state and once in the B state,
which gives VA and VB. From that you can compute
V(lambda) = lamda VB + (1-lambda) VA. And dv/dl = VB-VA. This is then
the QM and coulombic QM/MM contribution to dv/dlambda. The lennerd jones
should work automatically.
But this works only if you are not modifying the charges of the MM
atoms. Then things get more messy.
However, there is a problem with neighbour searching. Right now, the
QM/MM neighbour list is constructed only in the
if (!bFreeEnergy)
branch of the put_in_list function. I think this is why mdrun crashes.
the qmmm interface expects to find MM neighbours, but the QMMM nblists
are not created.
You can copy the if(bQMMM) branch into the free energy branch.
Best,
Gerrit
Subject:
Re: [gmx-users] QMMM free energy
From:
Erik Lindahl <[EMAIL PROTECTED]>
Date:
Wed, 30 May 2007 17:34:59 +0200
To:
Discussion list for GROMACS users <gmx-users@gromacs.org>
To:
Discussion list for GROMACS users <gmx-users@gromacs.org>
Hi,
I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure
the main reason is that you cannot either mutate atom types or
decouple interactions gradually in the QM part of the system. Once
this is solved for a pure QM system it should be straightforward to
implement the QM/MM interface of it.
Cheers,
Erik
On May 30, 2007, at 5:30 PM, Robert fiske wrote:
With the original QM/MM implementation, free energy is currently not
possible (yet). From what you report, I guess that also with the
CPMD interface it does not work.
The CPMD interface is mostly plugged into the same setup as the other
QM interfaces, I was able to bypass the error by copying modifying
the free energy else statement to bypass the vdw calculations for the
case of bQMMM true (and generally try to have that code match the
bQMMM case of non free energy runs). But since my background is
Computer Engineering and not chemistry (Chemistry 101 is as far as I
got in formal training) I don't really know what should be done (I
assume since as you said it's not implemented yet although I don't
get a run time error that the results will be off).
Are QM/MM free energy calculations substantially different than MM
calculations, or is it just not implemented because no one has needed
to do QM/MM with free energy yet?
fiske
Gogonea Group
Cleveland State University
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Subject:
Re: [gmx-users] QMMM free energy
From:
"Robert fiske" <[EMAIL PROTECTED]>
Date:
Wed, 30 May 2007 12:00:29 -0400
To:
gmx-users@gromacs.org
To:
gmx-users@gromacs.org
I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure
the main reason is that you cannot either mutate atom types or
decouple interactions gradually in the QM part of the system. Once
this is solved for a pure QM system it should be straightforward to
implement the QM/MM interface of it.
One of the main things we plan to do with the free energy code (once I
can confirm I'm doing things right) is to modify the charge of the
quantum system for the lambda values, so atom types don't need to be
modified for this I believe, although I see how that could complicate
other types of free energy calculations. As for decoupling
interactions I don't know what impact that has for changing of charge.
For now, are there any major complications if all we want to do is
modify the charge from state A to state B (assuming the interaction
problems you mentioned aren't a problem)
fiske
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