[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
gmx3 at hotmail.com
Tue Aug 17 15:06:42 CEST 2010
Erik was too lazy to document this, I now added it to the manual.
Type 4 is identical to type 1, it is only there to distinguish improper from proper dihedrals.
Type 9 is identical to type 1, except that multiple entries in dihedraltypes will lead to
multiple functions on one dihedral.
From: alanwilter at gmail.com
Date: Tue, 17 Aug 2010 12:16:16 +0100
To: gmx-users at gromacs.org
Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
I've been looking at amber ff implementation of gmx 4.5 since I am familiar to Sorin's ffamber works and I am the developer of ACPYPE.
I noticed that proper dih are not converted to RB anymore (which's great for understanding) and to accomplish that apparently 2 new funct were added to the gmx code, namely 4 and 9.
Needless to say that I couldn't find anything about funct 4 and 9 in the current gmx manual.
I would appreciate more information about it. Among other things I would like to know, e.g., what funct 4 would have different from funct 1, since in the seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs.
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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