Re: AMBER: Minimization and MD input files

From: David A. Case <>
Date: Tue, 25 Sep 2007 12:27:37 -0700

On Tue, Sep 25, 2007, Su Nwe wrote:
> I'm trying to run a simple molecular dynamic "without solvent" on an
> organic molecule using Amber 9. I could neither do minimization nor
> molecular dynamics. I'm assuming that I made some errors in setting
> parameters.
> The following is my minimization input file.
> initial minimisation
> &cntrl
> imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=0
> /

The default in sander is ntb=1, that is, for a periodic box with solvent.
If you want a simulation "without solvent", you need to specific ntb=0.

> I tried running the system "with solvent". Both minimization and
> molecular dynamic works, but when I looked at the molecule (.mdcrd
> file) using VMD, the molecules were shooting out everywhere and moving
> so randomly.

This sounds correct: if you want the animation to look "nice" (with all the
molecules in the central unit cell,) you need to use the "image" command in
ptraj to re-pack everything into the central unit cell.

These may not be the only problems, but I hope they will get you going in the
proper direction.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 26 2007 - 06:07:24 PDT
Custom Search