[gmx-users] Introducing DUMMY atom and top file modification

Justin Lemkul jalemkul at vt.edu
Fri Jan 17 02:54:20 CET 2014

On 1/16/14, 12:11 PM, Golshan Hejazi wrote:
> Thanks Bjorn,
> These are all good info and for sure helpful. However, I am thinking there should be some easier way in GROMACS because there is "typeB    chargeB   " feature in gromacs top file which seems to be related to the B-state when doing thermodynamics integration.
> But I could not find any documentation how to modify it for charmm force field. this page for example is showing how to do it for a gromacs force field:
> http://compbio.biosci.uq.edu.au/education/Free-Energy_Course/2.hydration-fe.html
> I dont know how to modify the "bond, angle and dihedral" section!

The format is not force field-specific.  See manual section 5.7.4 for an 
example.  B-state parameters can be listed in the same way as the A-state 
parameters.  For bonds:

ai aj func b0_A kb_A b0_B kb_B


Explicit B states are only necessary for transforming molecules; they are no 
longer necessary for hydration free energies as shown in the tutorial linked above.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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