On 6/3/14, 4:56 AM, 라지브간디 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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
