On 04/08/11, "Justin A. Lemkul" <[email protected]> wrote: > > > Yun Shi wrote: > >Hi all, > > > >I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a > >Lennard-Jones interaction function was used for short-range vdw interactions. > > > > From the reference paper /A Biomolecular Force Field Based on the Free > > Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets > > 53A5 and 53A6/, I found that for example, > > > >when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 > >type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = > >0.747786 kJ/mol. So I wonder if this value is considered to be small enough > >to be ignored. >
You should pay attention to the column headings in table 7 so that you can compute the contribution correctly. However, the magnitude of the energy of any particular interaction is not really of any concern. The evolution of the system depends on the *forces*, and it is likely that the sum of the forces on any atom from all its repulsion interactions from atoms that are (say) 1.4nm to 1.5nm away is very close to zero, except in highly non-homogeneous spatial distributions of particles. In any case, the sum of that contribution will be much smaller than the other contributions. Mark > > > > >In addition, it seems not until 5 nm does the dispersion term become larger > >than the repulsion term in this case, so would turning on Dispersion > >Correction between, say 1.5 to 5 nm introduce more errors than turning it > >off? > > > > You should use the cutoff described the authors of the force field, in this > case rvdw=1.4. Unless you can demonstrate that by using a different value > you can achieve superior results, stick with the specifics of > parameterization. I have never seen ill effects of setting rvdw=1.4 and > using dispersion correction with this force field. > > -Justin > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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