On Mon, Jul 22, 2013 at 2:17 PM, Pengzhi Zhang <pzhang5.central.uh.edu>wrote:
> Hi,
>
> I am using Amber 10 sander to run molecular simulations. Now I want to do
> some tests on different ways to mimic van der Waals interactions. As far as
> I know, in amber, 6-12 Lennard Jones potential is used. Does anyone know
> whether I can make some modification to this potential, such as making it
> to
> 6-10-12 potential? Any help is appreciated.
>
The only way of doing this is by modifying the Amber source code. Have a
look at where the non-bonded interactions are computed in sander
(subroutine get_nb_energy in short_ene.F90 for PME in sander, egb.F90 for
GB in sander, gb_ene.F90 for GB in pmemd, and somewhere inside
get_nb_energy in pmemd (I'm not sure about the latter, since Amber 10 is
quite old and I don't have ready access to that version of the source code).
Especially when asking about source code modifications, it's probably best
to use the most up-to-date version of Amber available, or the number of
people that will be able to answer your questions will be limited.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 22 2013 - 12:00:04 PDT
