AMBER Archive (2008)

Subject: Re: AMBER: vdw 6-9 potential

From: fatima.chami_at_durham.ac.uk
Date: Tue Aug 26 2008 - 11:03:55 CDT

Thanks for replying

Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:

>
> it's probably easiest to test out changes using the GB routines.
so I ll have to run an implicit solvent to check
> you can look in egb.f and see where it is done there.
               f6 = cn2(ic)*r6inv
               f12 = cn1(ic)*(r6inv*r6inv)
               evdw = evdw + f12 -f6
r2inv = rinv*rinv
r6inv = r2inv*r2inv*r2inv

so f12 = cn1(ic)*(r6inv*r2inv*rinv) will be the new term

> keep in mind you
> might need to change the values in the prmtop files.
and I need to amend the constant cn1(ic) in prmtop file

I want to mention that further changes have to be in the respect to use PMEMD
not Sander
best wishes
Fatima
>
> On Sat, Aug 23, 2008 at 6:34 AM, <fatima.chami_at_durham.ac.uk> wrote:
> > Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:
> >
> >>
> >> you need to tell us more- are you good at programming and want to know
> >> which routine to start making changes? or are you asking if there is a
> >> way without writing new code?
> >>
> > thanks for replying.
> > I want to know which routine to start making changes ...this will be
> usefull
> > for further changes like using the exponential type potential instead.
> >
> > I dont think there is way without changing the analytical form of the
> potential
> >
> > best wishes
> > Fatima
> >
> >> On Fri, Aug 22, 2008 at 4:56 PM, <fatima.chami_at_durham.ac.uk> wrote:
> >> > Dear all,
> >> >
> >> > I came accross the vdw 6-9 terms potential for the non bonded
> interaction
> >> > which was parametrized recently for some Si contained molecules
> >> >
> >> > how can I implement this in Amber
> >> >
> >> >
> >> > any feedback
> >> >
> >> > best wishes
> >> > Fatima
> >> >
> >> >
> >> > -----------------------------------------------------------------------
> >> > The AMBER Mail Reflector
> >> > To post, send mail to amber_at_scripps.edu
> >> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> >> > to majordomo_at_scripps.edu
> >> >
> >>
> >>
> >>
> >> --
> >> ===================================================================
> >> Carlos L. Simmerling, Ph.D.
> >> Associate Professor Phone: (631) 632-1336
> >> Center for Structural Biology Fax: (631) 632-1555
> >> CMM Bldg, Room G80
> >> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> >> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> >> ===================================================================
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> >> to majordomo_at_scripps.edu
> >>
> >>
> >
> >
> > --
> > Dr. F.Chami
> > Science Lab.
> > Department of Chemistry
> > Durham University
> > South Road Durham, DH 1 4 LE
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> > to majordomo_at_scripps.edu
> >
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu