AMBER Archive (2003)

Subject: Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling

From: Alfonso Garcia Sosa (atg21_at_hermes.cam.ac.uk)
Date: Tue Aug 05 2003 - 16:12:10 CDT

Yes, that solved it. I hadn't changed the modified NONB parameters in
the .frcmod file from those of the standard atom type, and so no
interactions were being picked up. Thanks a lot to David Case 

--
Alfonso T Garcia-Sosa

On Tue, 5 Aug 2003, David A. Case wrote:

> On Tue, Aug 05, 2003, Alfonso Garcia Sosa wrote:
> >
> >  I have been running some free energy perturbations
> > (thermodynamic integration, dynamically modified windows) with
> > electrostatic decoupling in gibbs (that came with amber7) and
> > had no problems during the first leg, ielper = 1, that is,
> > change in electrostatics and nothing else. For the second leg
> > (change in vdW and other non-electrostatics, fixed electrostatics),
> > I set ielper = -1, and started a new run. The problem I have is that
> > the values for energy changes are all zero for the whole length of
> > the new run and also after completion.
>
> >  Quantities used in integration:
> >     <dV/d_lam> = 0.38978385E-15 <V(lam-dep.)> = 165.62357
>
> Is it possible that your unperturbed and perturbed systems differ only
> in their charges?  This would explain getting zeroes for <dV/d_lam> and
> for the total change.
>
> This is just a wild speculation...otherwise, I don't see what is going on.
> If this isn't the problem, try just regular TI (without the dynamically
> modified windows), e.g. idifrg=1, isande=1, just asking for a single
> window.  You'll need just a few integration steps to see if you are still
> getting all zeroes...
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case                     |  e-mail:      case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
> The Scripps Research Institute    |  phone:        +1-858-784-9768
> 10550 N. Torrey Pines Rd.         |  home page:
> La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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