AMBER Archive (2007)

Subject: Re: AMBER: Minimization and MD input files

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 25 2007 - 14:27:37 CDT

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.

....dac

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