On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Amit Choubey wrote: > >> Hi all, >> >> I am trying to do a calculation on an artificial line charge in vacuum. >> The line charge has 267 atoms and each atom has a 1e charge. The atoms are >> bonded by a bond term and an angle term. I defined the required itp >> > > If you're trying to keep the atoms in a line, the system will not be > stable. Angles of 180 degrees routinely crash. Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ? > > files and top file. When i issue >> >> grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp >> >> I get the following error message. >> >> Program grompp_jpt, VERSION 4.5.3 >> Source code file: grompp.c, line: 175 >> >> Fatal error: >> The largest charge group contains 267 atoms. The maximum is 32. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> >> What should i try to do to circumvent this error. >> >> > The maximum charge group size is defined in the include/types/nblist.h > header. You can alter the value there, which will get around the error, but > consider whether or not this is even a good physical model. If all atoms > are in the same charge group, there are no electrostatic interactions > between these atoms since neighbor searching is done and short-range > energies are calculated based on inter-charge group distances. I have no > idea how to properly simulate a line of positively-charged particles, but be > aware. > Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials. > > -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<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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