Thanks Justin, I can see that there is no problem when i fix the periodicity.
Amit On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> I am doing dppc-water simulation. I am using structure and topologies from >> >> http://moose.bio.ucalgary.ca/**index.php?page=Structures_and_**Topologies<http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies> >> >> In version 4.0 when i do grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp >> -p system.top >> >> it creates npt.tpr without any errors. >> >> Using the same structure and topologies when i issue >> >> grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top >> >> it gives out the following warning >> >> Largest charge group radii for Van der Waals: 5.354, 5.297 nm >> Largest charge group radii for Coulomb: 5.354, 5.297 nm >> WARNING 1 [file npt.mdp]: >> The sum of the two largest charge group radii (10.650990) is larger than >> rlist (1.200000) >> >> I dont think the charge group should be so big. Can someone suggest what >> is going on ? >> >> > The input file contains broken molecules. There is nothing wrong, per se, > but only in the case when molecules are split across periodic boundaries. > This is a new check as of version 4.5. > > -Justin > > Ami >> >> > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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