> > OK, Pr van der Spoel, > So what is the correct way to obtain LJ C6 and C12 values given in the [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values.
If understand well [ atomtypes ] section give the comb-rules for the atom with itself, correct ? And the nonbond_types section, the comb-rules with the other atoms types. So if I take into account only the OM atom, as an example, why I obtained different values for C6 and C12 terms in the [ atomtypes ] section. Thank you again for your help. SA > ------------------------------ > > Message: 2 > Date: Mon, 28 Mar 2011 14:13:44 +0200 > From: David van der Spoel <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] Re: mathematical expression to obtain the C6 > and C12 LJ terms for the GROMOSXX ff family > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d907b78.20...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2011-03-28 14.07, sa wrote: > > 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 > Difficult to compare this way. > note that gromos does not use simple combination rules. > For OM there are different C12 (IIRC) depending on the interacting atom. > You should look only at the > [ nonbond_types] > section > > > > So your advices are welcome. > > > > SA > > > > > > 2011/3/28 sa <sagmx.m...@gmail.com <mailto: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 <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > > > >
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