From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Oct 31 2010 - 08:43:45 CDT
Dear Ipsita,
An atom moving from one side to the other is in itself not a problem. This
is because you are running the simulation in a periodic cell.
To ascertain the source of your "bad global exclusion," dump your dcd frames
and energies every step:
dcdfreq 1
outputEnergies 1
It is likely that your problem is either structural, residing in the
coordinates, or the topology. To determine which, dump the frames and
energies every step to try capture any problems with the coordinates.
Otherwise, the problem is likely in your psf topology.
Best,
Chris
On Wed, Oct 27, 2010 at 1:00 AM, ipsita basu <ibasu788_at_gmail.com> wrote:
> Sorry to bother you again, but I really can't understand why the water
> molecules appear in the other side of the cell, and one more thing is
> that if I allow to run the minimization, the job is running normally
> giving no warning and when I see the snapshot I found that the bilayer
> is perfectly allright but all the waters are in same side. The input
> is already attached. I would be really very grateful if you could
> provide me some help.
>
> ---------- Forwarded message ----------
> From: ipsita basu <ibasu788_at_gmail.com>
> Date: Fri, 8 Oct 2010 16:30:41 +0530
> Subject: namd-l:
> To: namd-l <namd-l_at_ks.uiuc.edu>
>
> Hi all,
> I am trying to minimize a lipid-bilyer system using namd, but
> during minimization the waters from one leaflet appears to be on the
> other side and then the job was terminated giving error like
> Bad global exclusion count, possible error!
> Increasing cutoff during minimization may avoid this.
> But I increase the cutoff and reduce the cell size but it doesnot
> change. I attach my input here.
> Is there anyone to help me? Please help me.
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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