[gmx-users] Non-bonded Interactions
라지브간디
rajiv at kaist.ac.kr
Tue Jun 3 10:56:40 CEST 2014
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 ?
On 5/31/14, 8:43 AM, ????? wrote:
> Dear justin,
>
> Could tell me how do I convert those non-bonded values between CHARMM and gromos431 ?
>
> I am unaware of this conversion.
>
Just for clarity, converting between CHARMM FF parameters to the Gromos FF will
result in a junk simulation. Converting CHARMM units for use in Gromacs
software (note the difference between Gromos and Gromacs!) is simple:
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
Epsilon: multiply the CHARMM value by 4.184 to convert kcal/mol to kJ/mol
-Justin
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