[gmx-users] Non-bonded Interactions

[Justin Lemkul]

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
>
>
> Please advice if i am making any mistake ?
>

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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