Fwd: minimization problem

From: ipsita basu (ibasu788_at_gmail.com)
Date: Fri Oct 29 2010 - 00:25:58 CDT

---------- Forwarded message ----------
From: ipsita basu <ibasu788_at_gmail.com>
Date: Wed, 27 Oct 2010 11:30:23 +0530
Subject: namd-l: minimization problem
To: namd-l <namd-l_at_ks.uiuc.edu>

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
-- 
Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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