Tutorial-l Mailing List
From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Mon Jan 29 2007 - 10:59:42 CST
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My guess is that there is something wrong with either the molecule geometry or the parameters used for the simulation. Check the log file to identify which energy term (bonds, angles, etc.) is larger than normal and investigate the possible source for that. Also view the molecule in VMD.
Ana
________________________________
From: owner-tutorial-l_at_ks.uiuc.edu on behalf of GUO HAO
Sent: Mon 1/29/2007 11:50 AM
To: tutorial-l_at_ks.uiuc.edu
Subject: tutorial-l: a question about small molecule
Hi, everyone. I am a new user of NAMD. When I use NAMD to do a minimization on a small molecule, its potential energy becomes to 99999999.9999 kcal/mol and cannot be reduced. Could you tell what I should do to figure it out? Thanks for your patience! Any suggestions are appreciated!
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