AMBER Archive (2003)

Subject: Gibbs: Electrostatic Decoupling

From: Paula Petrone (ppetrone_at_atlas.lanl.gov)
Date: Tue Feb 18 2003 - 11:31:41 CST

Hi.
I am running a gibbs calculation using electrostatic decoupling.
I got my output and .rst files using electrostatic decoupling IELPER = 1,
and lamda: 1) -> 0).
Now that charge has "vanished", I want to run the Van der Waals
perturbation on the same system using IDIEL = +1, to make the Van der Waals
spheres disappear.
I restart my system using as PINCRD filed the Gibbs.rst file I got from
the first procedure, setting IELPER=-1.
Gibbs Manual says that the second procedure should go:
LAMBDA(vdw) = 1, followed by van der Waals LAMBDA = 1 -> 0

My problem is that Gibbs doesn't realise it has to start again with
LAMBDA=1 for VVW even if I explicitly state ALMDA = 1.0.
so the result is that it only runs 1 step with LAMBDA=0 and stops.

how do I tell AMBER to start with LAMBDA = 1 again for VVWaals?
should I moidify the gibbs.rst file that states that LAMBDA=0?
should I run it reverse? Is it the same?

Thanks a lot.

------------------------------------------------------
Paula M. Petrone
Graduate Research
Assistant

MS K710, T-10
Theoretical Division
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505/665-0748
Fax: 505/665-3493
E-mail: ppetrone_at_lanl.gov

On Tue, 18 Feb 2003, Lishan Yao wrote:

> Hi:
> I am doing MD simulation for my protein ligand complex. I wonder whether I
> can find the energy representing ligand protein interaction in amber output
> files?
>
> Sincerely
> Lishan Yao
>
>
>