[gmx-users] Using lennard jones and buckingham terms simultaneously
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 23 17:12:00 CET 2010
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.
> 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.
> Gareth Tribello wrote:
>> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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