Matthew Watkins wrote:
Hi Gareth,
as Vitaly suggested tabulated potentials seem to be the only way to go,
it took me a while to get up to speed on the Gromacs way of doing this,
so get in touch if you wish.
I don't mean to hijack the thread, but this sort of thing would make an
excellent "How-To" on the Gromacs wiki site, if you have time to contribute it.
Tabulated potentials seem to frustrate many users. Although there are a
number of threads in the list archive with excellent information, it would be
great to have a wiki page for it all instead of piecing it together from
(sometimes incomplete) posts.
-Justin
The tables for buck potentials need to include the standard 1/r6 term
whilst what would be the 1/r12 term needs to contain exp(-Bx.rho), the
C6 and C12 coefficients can then be put in a standard nonbonded section.
You'll need a separated table for each pair of interactions that
interact with buckingham potential. Each pair must be an energy group
as well.
If there is a simpler method I'd love to hear it.
Cheers,
Matt
Gareth Tribello wrote:
Hello
I would like to use gromacs-4 to do a simulation of a small protein in
water and in the presence of calcium carbonate. The potential I have
for the calcium carbonate uses Buckingham terms for the interaction
between the calcium and carbonate ions, while the protein obviously
interacts through Lennard Jones terms. It is my understanding from
the manual that it is not possible to mix these two interaction types
and so it is not possible to do this simulation. Also when I
attempted to mix lennard jones and buckingham terms in a topol.top
file grompp complained.
Is there anyway around this problem?
Many thanks
Gareth
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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