Hi AMBER developers,
I am following up on this older post on the non-bonded interactions
calculation in amber 10.
I am trying to modify the non-bonded 6-12 L-J interactions for a number of
pairs of
pseudo-atoms that I have defined.
I see that the calculation of the 6-12 L-J terms is in the short.ene.f and
in particular in the
ew_directe.h header file that is included in the short_ene.f subroutine.
In previous versions of amber, the calculation was done separately for
periodic boundary conditions and for non-periodic systems.
Is this still the case for AMBER 10? And if yes, can you give me any hints
as to where does this distinction takes place?
I would really appreciate your help,
Thank you
On Mon, Aug 3, 2009 at 2:28 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Rizwan,
>
> See extra_pts.f for the 1-4 interactions for Ewald / PME runs etc.
> See ephi() in ene.f for the 1-4 interactions for GB etc.
>
> See short_ene() in short_ene.f for VDW in Ewald / PME runs etc.
> See short_ene_dip() in short_ene.f for VDW in Ewald / PME runs with
> polarizable force fields.
> See egb() in egb.f for the VDW interactions for GB runs.
>
> Good luck,
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Rizwan Tai
> > Sent: Monday, August 03, 2009 10:13 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Lennard Jones potential
> >
> > Hello, I am an undergraduate research student. I'm working with Amber 6
> > and
> > Amber 9. Can someone please help us find Lennard Jones subroutine. If
> > anyone
> > knows which file to look into, can you please help us?
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
Antonios Samiotakis
Department of Physics
University of Houston
4800 Calhoun Rd
SR1 Rm 629G, Houston
TX, 77204
e-mail: asamiotakis2_at_uh.edu
http://www.phys.uh.edu/~mscheung/antonios.htm
Tel: 713-743-3725
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Received on Thu Mar 18 2010 - 17:00:05 PDT
