Md at NVE

From: A.Madhumalar <>
Date: Sun 5 Nov 2000 16:29:40 +0400 (RET)

Dear amber users,
 I did MD at NVE conditions,for that i equilibrated the system at NVT
condition.Having done 10ps md .NVT condition,when i
viewed the system with water molecules,i found some water layers were
missing.I just wonder what is happening in the system!!can anyone suggest
what is actually happening?
Thanks for any replies

From Ryan.H.Lilien_at_Dartmouth.EDU 06 Nov 2000 15:38:49 EST
Message-id: <36789966.dasher.Dartmouth.EDU>
Date: 06 Nov 2000 15:38:49 EST
From: Ryan H. Lilien <Ryan.H.Lilien_at_Dartmouth.EDU>
To: AMBER list <>
Subject: Improper Dihedrals
In-Reply-to: < Sander/MPI/redimension>

  I'm emailing to ask about the implementation of improper dihedrals in the AMBER force-field. I have read through the parm.dat ( webpage file format description but have been unable to determine which atoms I,J,K, and L refer to. In some forcefields I is the central atom and in others, J is the central atom. So I essentially have two questions:

1. Which atoms are I, J, K, and L in the improper dihedrals

2. Is the standard cos terms used for these dihedrals or is another approach used.

Ryan Lilien
Department of Computer Science
Dartmouth College
Hanover, NH 03755
Received on Sun Nov 05 2000 - 04:29:40 PST
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