Re: [AMBER] Spreading water molecules over the simulation time

From: Daniel Roe <>
Date: Thu, 18 Jun 2015 09:18:17 -0600


On Wed, Jun 17, 2015 at 1:40 PM, Morteza Chehel Amirani <> wrote:

> Hello everyone
> I have performed a routine MD simulation in a water box with the periodic
> boundary conditions. When I load the output trajectory (with mdcrd format)
> in Chimera, it seems there is no box and water molecules spread in the
> space over the simulation time and the box is no more realized. I'm just

My guess is that you did not enable wrapping of coordinates (iwrap=1). What
you see is the waters diffusing into neighboring cells, but rest assured
the simulation is fine. As previously mentioned this is a visualization
artifact and can be corrected with the 'autoimage' command in cpptraj.


> wondering if anyone knows whether the problem is with the visualization of
> the results or something is wrong with the simulation parameters.
> Sincerely
> *Morteza Chehel Amirani*
> PhD Candidate
> Department of Mechanical Engineering
> University of Alberta
> 6-29 Mechanical Engineering Building
> Edmonton, Alberta, T6G 2G3
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 18 2015 - 08:30:03 PDT
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