That looks like (at least) a grompp bug leading to the error. Can you attach a .tpr file to http://redmine.gromacs.org/issues/1164 please Francesco?
Mark On Tue, Feb 26, 2013 at 8:09 PM, Justin Lemkul <[email protected]> wrote: > > > On 2/26/13 2:06 PM, francesco oteri wrote: > >> 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<https://docs.google.com/file/d/0B1ktZ-u2OHFAdUl6UkFJajNGcGs/edit> >> > >> >> processed.top<https://docs.**google.com/file/d/0B1ktZ-** >> u2OHFAcG82WnltVmdFN1U/edit<https://docs.google.com/file/d/0B1ktZ-u2OHFAcG82WnltVmdFN1U/edit> >> > >> >> 01em.gro <https://docs.google.com/file/**d/0B1ktZ-** >> u2OHFAZ0d3WGs3U1dBaU0/edit<https://docs.google.com/file/d/0B1ktZ-u2OHFAZ0d3WGs3U1dBaU0/edit> >> > >> >> index.ndx<https://docs.google.**com/file/d/0B1ktZ-** >> u2OHFAemxNc0c5YlRlNlE/edit<https://docs.google.com/file/d/0B1ktZ-u2OHFAemxNc0c5YlRlNlE/edit> >> > >> >> > Perhaps the previously fixed issue isn't perfect, but again this is the > same symptom where apparently rlistlong is not being fully interpreted. > There should be nothing wrong if you have an adequate setting for > rlistlong. > > -Justin > > > >> >> 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<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<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> >>>>>> > >>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>>> Mailing_Lists/Search<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> >>>>>> <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> >>>>>> <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://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> >>>> > >>>> >>>> >>> >>> >>> -- >>> Cordiali saluti, Dr.Oteri Francesco >>> >>> >> >> >> > -- > ==============================**========== > > > 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? 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