Re: [AMBER] First to Second Frame Position Jump

From: Daniel Roe <>
Date: Wed, 10 Jul 2013 21:31:27 -0600


On Wed, Jul 10, 2013 at 5:45 PM, Parker de Waal
<> wrote:
> and density additions) my protein and ions seem to jump drastically causing
> a very large rmsd. Additionally it seems that my ions are clumped together
> on the first frame and re-enter the solution during the second frame.

Are these jumps that you see accompanied by corresponding jumps in the
energy? Is your simulation crashing and/or do you have '*****' in your
coordinates or printed energies? If not then it could be you just have
visualization artifacts caused by imaging; these artifacts can be
removed with the 'autoimage' command of cpptraj.

On another note, your ions should never be "clumped" together. If they
are built in that way for some reason you can use the 'randomizeions'
command of ptraj/cpptraj to randomize the initial ion positions. Also,
if you are using monovalent salt make sure you are using the
Joung/Cheatham ion parameters.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jul 10 2013 - 21:00:03 PDT
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