[gmx-users] Non-bonded Interactions

[라지브간디]

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