> > Thank you Justin for your response > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command
g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6 = 4.66239e-03, c12 = 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen) Did I miss something ? Thank you again for your help SA > sa wrote: > > Dear All, > > > > I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff > > for a new atom type and incorporate them in my ffnonbonded.itp. Does > > anybody know the mathematical expressions used to obtain these terms > > from a sigma (nm) and an epsilon (kj/mol) values manually. > > > > g_sigeps can do this for you. Otherwise, you can convert between the two > common > forms of the Lennard-Jones equation. > > -Justin > > > Thank you for your help. > > > > SA > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > >
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