thanks Justin, best regards,
2013/3/5 Justin Lemkul <[email protected]> > > > On 3/5/13 7:48 PM, fciocco wrote: > >> Hi, >> >> I have a quick question: >> >> the ;; lipid-SPC/SPCE interactions section : >> LO OW 1 2.50200e-03 2.06700e-06 >> LOM OW 1 2.50200e-03 2.06700e-06 >> LNL OW 1 2.98000e-03 3.25900e-06 >> LC OW 1 3.59800e-03 6.04400e-06 >> LH1 OW 1 3.26800e-03 5.71200e-06 >> LH2 OW 1 4.30700e-03 8.17000e-06 >> LP OW 1 4.92600e-03 8.21000e-06 >> LOS OW 1 2.60500e-03 2.24100e-06 >> LP2 OW 1 3.94400e-03 7.80300e-06 >> LP3 OW 1 4.82100e-03 9.53900e-06 >> LC3 OW 1 4.97800e-03 9.85000e-06 >> LC2 OW 1 3.96900e-03 6.93800e-06 >> >> in the [ nonbond_params ] section in lipid.itp file downloaded from >> Tieleman's site should be include in the ffnonbonded.itp file? >> >> the KALP-DPPC tutorial says: In the [ nonbond_params ] section, you will >> find the line ";; parameters for lipid-GROMOS interactions." Delete this >> line and all of the subsequent lines in this section; but I'm not 100% >> sure >> if I have to delete the lipid-SPC/SPCE interactions lines. >> >> > The C6/C12 parameters for the OW atom type are slightly different in 53A6 > than they were in Gromos87 (looks like mostly rounding differences in the > nonbonded parameter files). The parameters listed in lipid.itp are based > on Gromos87, so if you're using 53A6, then do as the tutorial says and > delete the lines. The necessary interactions will simply be calculated > according to normal combination rules. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
