Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom.
OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07 So your advices are welcome. SA 2011/3/28 sa <sagmx.m...@gmail.com> > 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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