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

From: windy <>
Date: Thu, 18 Jun 2015 09:30:28 +0800 (CST)

You can use 'autoimage' for projecting the water to the original box

see AmberTools

在2015年06月18 03时40分, "Morteza Chehel Amirani"<>写道:

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
wondering if anyone knows whether the problem is with the visualization of
the results or something is wrong with the simulation parameters.

*Morteza Chehel Amirani*
PhD Candidate
Department of Mechanical Engineering
University of Alberta
6-29 Mechanical Engineering Building
Edmonton, Alberta, T6G 2G3
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Received on Wed Jun 17 2015 - 19:00:03 PDT
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