On 6/4/14, 7:27 AM, 라지브간디 wrote:
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])
?
Neither. I have said it twice before, and I'll say it a third time - the
parameters you have cannot be sensibly combined with others in the Gromos96 43A1
parameter set. They were developed for CHARMM; they need to be used with a
CHARMM force field. Hacking them into some other force field breaks the
internal self-consistency of the force field and you end up with a junk simulation.
The proper approach is to introduce the parameters in [atomtypes] of
ffnonbonded.itp in the CHARMM force field and let the combination rules do the
rest of the work.
-Justin
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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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