AMBER Archive (2006)

Subject: Re: AMBER: Distortion in parallelploied

From: Angelo Pugliese (
Date: Mon Feb 13 2006 - 09:40:40 CST

With the "image" action you have to specify the "familiar" keyword,
after when you use VMD you should see your original box shape

Varsha Goyal wrote:

>I generated my topology file and coordinate files.
>After that i minimized my system and heated upto 300K
>at constant volume. now when i am trying to run MD
>using Sander my solvent box is getting distorted.
>My input file is:
>Molecular Dynamics run
> imin=0, iwrap=1,ntx=5, ntf=1, cut=15.0,
> ntpr=100, ntwx=100,
> ntb=2, ntp=1,iwrap=1,
> nstlim=100000, dt=0.001,
> tempi=325.0, temp0=325.0, ntt=1,
>And attatched in picture of distorted box
>Please suggest me whether something is going wrong. I
>am using periodic bounday conditions and using VMD for
>Find your next car at

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to