AMBER Archive (2006)

Subject: Re: AMBER: Distortion in parallelploied

From: Angelo Pugliese (angelo_at_holmes.cancres.nottingham.ac.uk)
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:

>Hello,
>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
>&cntrl
> 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
>visualization.
>Thanks,
>Varsha
>
>
>
>
>
>
>__________________________________________________________
>Find your next car at http://autos.yahoo.ca
>

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