@Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:46 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: > 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 -- 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
