AMBER Archive (2006)

Subject: AMBER: Distortion in parallelploied

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Thu Feb 09 2006 - 19:39:06 CST

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

        

        
                
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