[gmx-users] Conversion of charmm36 parameters from namd to gromacs

Justin Lemkul jalemkul at vt.edu
Tue Dec 5 03:21:14 CET 2017

On 12/4/17 2:35 PM, Daniel Bauer wrote:
> Unfortunatly It seems like my university has no contract to access this
> paper so I cant check the SI.
> The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted
> to better match the free energy of solvation in NMA).

There seem to be several layers of assumption here, including targeting 
a value that is actually unknown.

If you want to compare, in the paper I linked before, we did a QM 
potential energy scan for NMA...K+ as a function of the distance between 
the carbonyl O and the ion. The standard CHARMM force field parameters 
are too weak by about 6 kcal/mol relative to an MP2/6-311++G(2df,2pd) 
energy surface. The NBFIX we applied to correct it was:

epsilon = -0.050218 kcal/mol
Rmin = 3.30375 A


> On  12/04/2017 07:53 PM, Justin Lemkul wrote:
>> On 12/4/17 12:21 PM, Daniel Bauer wrote:
>>> Hello,
>>> I finally found my error in the conversion. As always, the devil is in
>>> the detail. I was under the assumption that parameters listed in the
>>> original forcefield files (toppar) are also sigma and epsilon values.
>>> However, as you know, the original files list Rmin values (and not
>>> sigma).
>>> With the correct conversion term:
>>> eps = Rmin/(10*2^(1/6))
>>> I can now reproduce the conversion of the numbers from the charmm
>>> implementation to gromacs (and thus know how to apply my NBFIX for this
>>> value).
>> I don't know what NBFIX you might have, but FYI there is a value that
>> will become official in the next release of the force field. We've
>> validated it against proteins and nucleic acids. See the SI of
>> http://dx.doi.org/10.1128/AAC.01572-17
>> -Justin


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list