[gmx-developers] free energy with urey-bradley

[Shirts, Michael (mrs5pt)]

I was discussing with Michel about this, and I can go ahead and add this to
the free energy code I've been working on in 4.6 (which I am probably going
to try to add in next week if I can figure out the right way to manage the
gerrit issues . . . .)

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Sat, 29 Oct 2011 10:30:49 +1100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] free energy with urey-bradley
> 
> On 29/10/2011 7:17 AM, Michel Cuendet wrote:
>> 
>> 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 !
> 
> 
> I'd guess it is an historical accident - U-B was implemented many years
> before CHARMM forcefield was added. Table 5.5 correctly notes that U-B
> cannot be interpolated in free energy calculations. It looks fairly
> straightforward to add such interpolation.
> 
> Mark
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