[gmx-developers] free energy with urey-bradley

Michel Cuendet michel.cuendet at isb-sib.ch
Fri Oct 28 22:17:53 CEST 2011

Hi Gromacs People,

I'm trying to set up a thermodynamic integration simulation with the 
charmm force field to calculate the free energy of mutating a side chain 
to another (similar) one. But apparently, the urey_bradley parameters 
for topology B are not taken into account... I checked in the code and 
we have :

in ifunc.c  (l.105) :
def_angle   ("UREY_BRADLEY","U-B",          3, 4, 0,  0,          
urey_bradley ),
meaning zero parameters are read for the B topology.

and in bondfree.c (l.835) :
     *dvdlambda += harmonic(kth,kth,th0,th0,theta,lambda,&va,&dVdt);  
/*  21  */
     *dvdlambda += harmonic(kUB,kUB,r13,r13,dr,lambda,&vbond,&fbond); 
/*  19  */
meaning the same parameters are used for both A and B.

Is there a particular reason for which the lambda-interpolation of the 
urey-bradley term was not implemented?

Has anyone implemented it in a development version?

There should at least be a warning in grompp about this !


Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne

More information about the gromacs.org_gmx-developers mailing list