oops ! Yes, thanks a bunch !
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, February 06, 2015 2:10 PM
To: AMBER Mailing List
Subject: Re: [AMBER] protein falls apart on explicit solvation md
Hi,
Looks like you tried to load 'Amber Coordinates' when you actually
need 'Amber Coordinates with Periodic Box'. To avoid this issue in the
future use NetCDF trajectories (ioutfm=1).
-Dan
On Fri, Feb 6, 2015 at 1:04 PM, Anupam Goel <goelan.uab.edu> wrote:
> Hi all,
>
> I am running explicit solvent simulation for the first time and my structure falls apart. Has anyone noticed such behavior before? Please suggest troubleshooting.
>
> I am attaching a picture of what the trajectory looks like on vmd. Also, attaching mdcrd, prmtop and other associated files.
>
> Thanks,
> AG
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 06 2015 - 12:30:04 PST
