I downloaded and installed gromacs-4.6 but I get the warning WARNING 1 [file NVE.mdp]: The sum of the two largest charge group radii (0.067845) is larger than rlist (1.200000) - rvdw (1.200000)
I attacch the files you may need to solve the problem NVE.mdp <https://docs.google.com/file/d/0B1ktZ-u2OHFAdUl6UkFJajNGcGs/edit> processed.top<https://docs.google.com/file/d/0B1ktZ-u2OHFAcG82WnltVmdFN1U/edit> 01em.gro <https://docs.google.com/file/d/0B1ktZ-u2OHFAZ0d3WGs3U1dBaU0/edit> index.ndx<https://docs.google.com/file/d/0B1ktZ-u2OHFAemxNc0c5YlRlNlE/edit> 2013/2/26 francesco oteri <[email protected]> > Thank you so much for the help! > > > 2013/2/26 Justin Lemkul <[email protected]> > >> >> >> On 2/26/13 12:01 PM, francesco oteri wrote: >> >>> I am using 4.5.5...Is it OK? >>> >>> >> If it's giving a note about that, then clearly not. Try 4.6. But as I >> said, there's nothing actually wrong. >> >> -Justin >> >> >>> 2013/2/26 Justin Lemkul <[email protected]> >>> >>> >>>> >>>> On 2/26/13 11:47 AM, francesco oteri wrote: >>>> >>>> Thank you Justin, >>>>> I added >>>>> rlistlong = 1.4 >>>>> >>>>> but still grompp complains: >>>>> NOTE 1 [file 02md.mdp]: >>>>> For energy conservation with switch/shift potentials, rlist should >>>>> be >>>>> 0.1 >>>>> to 0.3 nm larger than rvdw. >>>>> >>>>> Why doesn't grompp looks for rlistlong value? >>>>> >>>>> >>>>> There was a problem with an older version of Gromacs (I can't remember >>>> which) where grompp ignored rlistlong. It has no implication for mdrun >>>> and >>>> is solved by using the newest version. >>>> >>>> >>>> -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://vt.edu/Pages/Personal/justin> >>>> <h**ttp://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> >>>> <htt**p://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<h**ttp://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> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> >>> >>> >> -- >> ==============================**========== >> >> 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> >> > > > > -- > Cordiali saluti, Dr.Oteri Francesco > -- Cordiali saluti, Dr.Oteri Francesco -- 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
