sorry i did not mention it but the E field contribution should be zero, i am sure about it. Also when i make all the cutoff = 0 the energy terms are Step Time Lambda 0 0.00000 0.00000
Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.11496e-07 0.00000e+00 0.00000e+00 1.03128e+06 1.03128e+06 Pressure (bar) 0.00000e+00 Step Time Lambda 1 1.00000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 7.49142e-02 0.00000e+00 0.00000e+00 1.03104e+06 1.03104e+06 Pressure (bar) 0.00000e+00 Coulomb (SR) is quite close but not exactly equal to previous case when cutoff is 60 nm. On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Following is the mdp file >> >> cpp = /usr/bin/cpp >> ;define = -DFLEX_SPC >> constraints = none >> integrator = steep >> nsteps = 10000 >> ; >> ; Energy minimizing stuff >> ; >> emtol = 200 >> emstep = 0.01 >> pbc = no >> nstcomm = 0 >> ns_type = grid >> coulombtype = Cut-off rlist = 60 >> rcoulomb = 60 >> rvdw = 60 >> Tcoupl = no >> Pcoupl = no >> gen_vel = no >> >> E_x = 1 0 0 >> E_y = 1 0 0 >> E_z = 1 0 0 >> >> >> Following is the energy term >> >> Step Time Lambda >> 0 0.00000 0.00000 >> >> Energies (kJ/mol) >> Bond Angle LJ (SR) Coulomb (SR) Potential >> 1.11496e-07 0.00000e+00 0.00000e+00 9.90561e+05 9.90561e+05 >> Pressure (bar) >> 0.00000e+00 >> >> Step Time Lambda >> 1 1.00000 0.00000 >> >> Energies (kJ/mol) >> Bond Angle LJ (SR) Coulomb (SR) Potential >> 7.55922e-02 0.00000e+00 0.00000e+00 9.90324e+05 9.90324e+05 >> Pressure (bar) >> 0.00000e+00 >> >> >> > I suspect that energy terms comes from the use of an electric field, which > you had not mentioned before. > > -Justin > > Amit >> >> >> On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Justin, when i define the whole line charge as a charge group i >> do get a coulomb energy contribution. I thought there would be >> no non-bonded contribution. I use a very high cut-off (longer >> than chain length) and no pbc. Am i missing something ? >> >> >> Without seeing your .mdp file and the actual energy terms you're >> observing, I can only guess. One would think that if it is the only >> molecule in the system, there should be no intermolecular Coulombic >> terms (unless maybe some arise due to periodicity, but in that case >> you do not have an infinite system and then they are artifacts). >> There may be intramolecular terms (like 1-4) or PME-related terms. >> >> -Justin >> >> On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey >> <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com> >> <mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>> wrote: >> >> I was not sure if changing the size of maxcg would not >> negatively >> influence anything else. I will give it a try. Thanks Justin >> >> >> On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Amit Choubey wrote: >> >> I change the maximum charge group size defined in the >> include/types/nblist.h header from 32 to 267. Then >> grompp >> worked fine but the mdrun did not start. The >> following error >> came out >> >> Program mdrun_jptlc, VERSION 4.5.3 >> Source code file: ns.c, line: 2417 >> >> Fatal error: >> Max #atoms in a charge group: 267 > 64 >> >> >> /* Verify whether largest charge group is <= max >> cg.* >> * This is determined by the type of the local >> exclusion >> type * >> * Exclusions are stored in bits. (If the type is >> not large* >> * enough, enlarge it, unsigned char -> unsigned >> short >> -> unsigned long)* >> */ >> >> >> The solution is described in the comment above. >> >> >> maxcg = sizeof(t_excl)*8; >> >> >> Increase the size here. >> >> -Justin >> >> >> if (nr_in_cg > maxcg) >> { >> gmx_fatal(FARGS,"Max #atoms in a charge >> group: %d > >> %d\n", >> nr_in_cg,maxcg); >> } >> >> >> -- ==============================**____========== >> >> Justin A. 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Use >> the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> > >> <mailto:gmx-users-request@__gr**omacs.org<http://gromacs.org> >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >>. >> >> 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. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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. 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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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