[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

Berk Hess 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

Hi there,
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.

Many thanks,
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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