Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics

From: David A Case <>
Date: Thu, 5 Mar 2015 08:12:44 -0500

On Thu, Mar 05, 2015, Zhang, Sixue wrote:
> I used autoimage command in cpptraj, it doesn't bring the box back to
> the rectangular shape as I defined.
> What else wrapping command can I try besides adding iwrap=1 in the input file?

Sounds like this is not a wrapping problem. What is the density of your
simulation? If it is much less than 1 gm/cc, you might be getting some odd
shapes. Otherwise, we would need to see a small example that illustrates the
problem (and allows us to reproduce it).


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Received on Thu Mar 05 2015 - 05:30:10 PST
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