[gmx-users] Non-bonded interactions

[라지브간디]

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