AMBER: Distortion in parallelploied

From: Varsha Goyal <>
Date: Thu, 9 Feb 2006 20:39:06 -0500 (EST)

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


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Received on Sun Feb 12 2006 - 06:10:08 PST
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