Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue.
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/1/13 10:33 PM, Xu Dong Huang wrote: >> Dear advanced gromac users, >> >> I am trying to simulate a long linear chain of polymer using CG beads. >> (about 200 beads), all with same type charge interactions. (examples shown:) >> I read on previous gromacs mailing list that linear systems with same >> charges make the system unstable? But is there anyway to go around that? >> > > It's the angles that make the system unstable. One can use virtual sites to > get around the issue. There is a trivial example in a tutorial I wrote: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html > > The bigger question is whether or not the angles in the molecule impose > linearity, or whether the initial configuration is simply a line of particles > that may deviate according to angle and dihedral potentials. You haven't > shown the [angles] or [dihedrals] directives, so it's not clear what you're > intending, exactly. > >> [atoms] >> 1 P3 O1 mon 1 0.00 >> 2 P3 O1 mon 2 0.00 >> 3 P3 O1 mon 3 0.00 >> 4 P3 O1 mon 4 0.00 >> 5 P3 O1 mon 5 0.00 >> 6 P3 O1 mon 6 0.00 >> 7 P3 O1 mon 7 0.00 >> 8 P3 O1 mon 8 0.00 >> 9 P3 O1 mon 9 0.00 >> ……. >> [ bonds ] >> 1 2 1 0.43 17000 >> 2 3 1 0.43 17000 >> 3 4 1 0.43 17000 >> 4 5 1 0.43 17000 >> …… >> >> However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr >> -it returns the error of: >> Fatal error: >> The largest charge group contains 200 atoms. The maximum is 32. >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> Please let me know if there is a way to go around that. Thank you. >> > > Do as the error message says and put fewer than 32 atoms in each charge > group. The size of the charge group has implications for neighbor searching > if using a group-based cutoff scheme. > > -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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
