Re: doubts

From: David A. Case <>
Date: Sat, 22 Mar 2003 08:56:11 -0800

On Fri, Mar 21, 2003, thenmalar rathinavelan wrote:

> I have following doubts. That is,
> (1) I wish to calcualte the free energy of formation
> of a DNA system. For that, I am carrying out steepest
> descent (1000cycles) and conjugate gradient
> minimization for the convergence of 0.0001 in vaccum.
> However, during the minimization following error
> occurs.
> 237700 -2.9549E+02 6.7657E-04 1.1241E-02
> C6 966

This is an excessive number of steps of minimization. If you truly
need an extrememly small gradient RMS, you may need to use the Newton-
Raphson technique in nmode. But the results above should be OK for
normal mode analysis. I can't say what caused the instability you

...good luck...dac

> (2) I have another basic question regarding prep and
> parm.dat files.
> For the dynamics or minimization bond distance,
> angle and torsional parameters given in parm
> (parm94.dat or parm.96.dat or ....) file are used.
> However, we are specifying bond length, angle and
> torsional angle values in the prep file also. I like
> to know whether prep values be overridden (except
> parital charges) by the values specified in the
> parm.dat file.

The prep files (are you still using those??) give the starting geometries.
These are not related to the values in the parm.dat files, which provide
the force field parameters (or target values) that will be used during
the simulation.

...hope this helps...dac

David A. Case                     |  e-mail:
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            |
Received on Sat Mar 22 2003 - 17:53:02 PST
Custom Search