AMBER Archive (2001)

Subject: Re: MD in vacuo

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Mon Nov 05 2001 - 14:27:23 CST

check the NTWXM variable in the manual, and related ones for the
other files. You need to set it to a small value like 1.

----- Original Message -----
From: "Lepsa" <lepsik_at_marilyn.uochb.cas.cz>
To: "AMBER Mail Reflector" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, November 05, 2001 1:52 PM
Subject: MD in vacuo

> Dear AMBER users,
> I have a simple task to run a molecular dynamics of a protein in vacuum. I
> use sander_classic with PME turned off.
> Strangely enough, I cannot get mdcrd, mdvel and mdene files out of it for
> the worlds. Could you please tell me what I am missing? (Do I need to put
in
> a cutoff value for nonbond interactions?)
>
> Thanks.
>
> Sincerely,
>
> Martin Lepsik
>
> P.S. My input looks like
>
> molecular dynamics in vacuum
> &cntrl
> imin=0, ntx=1, tempi=0.,
> ntt=1, temp0=300.0, tautp=0.2,
> nstlim=1000, scee=1.2, ntwv=100,
> ntwe=100, ntwx=100, ntpr=100,
> &end
>
> and moreover I have my coordinate and topology files
>
>