AMBER Archive (2004)

Subject: Re: AMBER: pmf calculation using gibbs.

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 19 2004 - 10:27:33 CST

On Thu, Feb 19, 2004, Myunggi Yi wrote:

> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.000 PRESS =
> **********
> Etotal = ************ Kinetic = 0.00000 Potential = ************
> Bond = 0.00000 Angle = 1.18748 Dihed = 0.00000
> 1-4 VdW = 0.00000 1-4 Elec= 0.00000 Van d Waal = ************
> Elect. = -1436.85936 H-bond = 0.00000 Constraint = 0.00000
> Ekcmt = 0.00000 VirT = ************ Volume = 20663.92973
> Density = 0.58458

I have a variety of suggestions. First, equilibrate you system in sander
before trying to run in gibbs. Find out why your van der Waals energy
at the first step is so bad (and why the bond, 1-4 energies, etc are zero);
examine the structure visually, and use the checkoverlap command in ptraj;
always equilibrate first at constant volume before going to constant pressure.

The tutorials give good advice about equilibration; try to do for your system
what is shown there.

...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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