Hi Rizwan,
The code has changed A LOT between amber 6 and amber 9 so you will have a
lot of work to do to merge things in. You might also want to consider doing
this with AMBER 10 instead of AMBER 9.
In AMBER 9 the essence is that runmd() calls force(). For GB calculations
this calls egb() which calculates the nonbond and GB terms. For explicit
solvent simulations this calls ewald_force which does the reciprocal and
direct space calculations. The direct space is via a call to get_nb_energy()
which is in short_ene.f
In short there is no way simple grepping for AMBER 6 variables is going to
help you. You need to trace through the code from force.f downwards into
get_nb_energy and associated routines.
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 9:13 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] nonbon.f question
>
> Hello,
>
> We have tried looking for " imin, ntt, ntu, idiel, ntb" using the grep
> command but could not find the nonbon subroutine in amber 9. Could you
> please tell us what are the subroutine for nonbon in amber 9. Or are
> there
> any words other than those mentioned above which might help us find the
> nonbon subroutine. We will appreciate a quick reply.
>
> Thanks
>
>
> On Mon, Jul 27, 2009 at 2:34 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > most of the files have multiple routines and they may not always be
> > moved to one file. its best to use grep to search for the name of
> the
> > subroutine that you want to modify.
> >
> > On 7/27/09, Rizwan Tai <rizwantai.gmail.com> wrote:
> > > Hello, We are transferring Amber 6 code to Amber 9. And we are
> trying to
> > > locate the nonbon.f file in Amber 9. Can you tell us where its
> located
> > and
> > > what it is called?
> > >
> > > --
> > > Every man, that Day, will have enough to make him careless of
> others."
> > > (Quran 80:37)
> > > _______________________________________________
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> > >
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Professor, Department of Chemistry
> > CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> > Stony Brook University E-mail: carlos.simmerling.gmail.com
> > Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> > ===================================================================
> >
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> >
>
>
>
> --
> Every man, that Day, will have enough to make him careless of others."
> (Quran 80:37)
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Received on Wed Aug 19 2009 - 20:18:34 PDT
