On 29/10/2010 10:14 AM, Sai Pooja wrote:
Hi,
I want to modify the contribution to Interaction energy of different
groups - say I have groups A and B and I want the energy to be scaled
as E_AA + 0.1E_AB + 0.5*E_BB. Interaction parameters of each of these
groups are set by a forcefield
Now after multiple correspondence on the gromacs list I have concluded
that there are 3 ways of doing this:
1. Using tables - for this I would have to list non-bonded parameters
for all atoms such that the combination rule and the table-potential
is used. For the table for BB interaction, scale the Coloumb and VdW
interactions in the tables by a factor of 0.5 and so on...
Sure. I think that for the above example, you'd need only 2 (maybe 3)
table files.
However, since tables would have to be supplied for pairs too
(tablep), it may not be accurate to supply 6-12 tables with coulomb
potential for these pairs. I am using CHARMM and the 1998 paper on
CHARMM says that in some specific cases the 1-4 interactions many be
scaled which makes me doubt this approach.
Yeah, something extra will be required here. Obviously, test and develop
on a small toy system that you can compute by hand in a spreadsheet.
2. Forcefield parameters - By defining scaled [nonbonded_params] for
all relevant atoms. This will change the VdW interactions, but not
sure about the Coulomb interactions.
The Coulomb interactions are based on atomic charges, and there's no
ready way to scale them differently for different interactions.
3. Modifying gromacs - by passing a parameter lambda to gromacs which
scales the force/potential by a factor lambda when gromacs calculates
force/potential.
For implementing option 3, which programs in the gromacs package would
be the bes tstarting points for editing the energy contributions of
different groups/atoms?
I can think of two ways of approaching this. Efficiency requires that
you use the energy group mechanism for your respective groups. Then you
need to identify the generated non-bonded lists and do the necessary
book-keeping to allocate scale factors to them. Then, either
a) pass the scale factor all the way into the non-bonded kernels and use
them suitably there, or
b) create a copy of the force and energy arrays for each required scale
factor, pass matching arrays into the appropriate kernels, and do the
scaling on the respective arrays after all kernel contributions have
been made, and then add the corresponding array elements.
Either way, you'll need a sound understanding of the code in
src/gmxlib/nonbonded.c (and the kernels it calls, and how its data
structures get created in the neighbour-searching). Make a test system,
like a dipeptide in a small box of water, with energy groups, and use a
debugger to see how things work.
a) is the easiest to develop. The kernels already have a "user data"
pointer you can use, and it would be a fairly simple matter to adapt the
generic C kernels to do your scaling. You will give up a lot of
performance, however, unless you are prepared to adapt the
hardware-optimized kernels similarly (not advised).
b) will use somewhat more memory, have a smaller code-change footprint,
keep essentially the same performance
As a more general question, how does one run a generalized Hamiltonian
REM on gromacs?
You can't. GROMACS REMD requires a normal MD Hamiltonian supplied in a .tpr.
Mark
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