# [gmx-users] Non-bonded Interactions

Justin Lemkul jalemkul at vt.edu
Tue Jun 3 14:33:33 CEST 2014

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On 6/3/14, 4:56 AM, 라지브간디 wrote:
> Dear Justin,
>
>
> I have calculated upon the way you provided as follows :
>
>
> CHARMM Rmin/2 -> Gromacs sigma:
> multiply by 2 to get Rmin, convert to sigma by
>
> multiplying by 2^(-1/6), then multiply by 0.1 to convert A -> nm
>
>
> Sigma = 3.83
> Rmin = (3.83 * 2)
>
>
> 7.66 * 2^(-1/6)*0.1 = 0.682428418
>
>
> Epsilon: multiply the CHARMM value by 4.184 to convert kcal/mol to kJ/mol
>
>
> Epsilon 0.0262 x 4.184 = 0.1096208
>
>
> Is that right conversion?, if so, I have used g_sigeps utility in gromacs for above mentioned sigma and epsion values and got entirely different values:
>
>
> g_sigeps -sig 3.83 -eps 0.0262
>
>
> c6    =  3.30791e+02, c12    =  1.04411e+06
> sigma =      3.83000, epsilon =      0.02620
> Van der Waals minimum at 4.29903, V = -0.0262
>
>
> Fit of Lennard Jones (12-6) to Buckingham:
>
> A = 4264.18, B = 2.79133, C = 330.791
>
>
>

You're not supplying the right values to g_sigeps.  It's designed to convert
known values of sigma and epsilon (already in Gromacs units) to C6/C12, which is
not what you need to accomplish.  The value you're passing to -sig is actually
Rmin, not sigma, and the value you're supplying to -eps is in the wrong units.

The converted values you obtained with by-hand calculation (not g_sigeps) appear
reasonable.  Verifying the energy reported by CHARMM/NAMD and Gromacs should be
a simple test to confirm.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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