[gmx-users] Non-bonded interactions
라지브간디
rajiv at kaist.ac.kr
Wed Jun 4 13:28:04 CEST 2014
Dear justin,
Shall I introduce this calculated non-bonded interaction values in gromos43a1.ff ( ffninbonded.itp) section or
specifically I can include them in my protein topology file ? ([nonbond_param]) ?
On 6/3/14, 4:56 AM, ????? 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
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