Of course, you can simulate what you like, but I would personally use an all-atom representation for long hydrocarbons. I think explicit hydrogens matter for conformations.
V.V. Chaban On Thu, May 23, 2013 at 5:16 PM, Bao Kai <paeanb...@gmail.com> wrote: > Hi, all, > > I finally wrote a decane topology file. I used it to some simple > simulation. > > The energy minimization works, while after a simple nvt equilibration, > the shape of the molecules changed. > > Please find the images before and after the nvt equilibration from the > following links. > https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png > https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png > > > > The following is the topology part for the decane molecule. Please > help to check if there is anything wrong. C2 and C3 are CH2 and CH3 > respectively. > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 3 yes 0.5 0.5 > > [ atomtypes ] > ; type at.num mass charge ptype sigma epsilon > C2 6 14.0270 0.0 A 0.374 0.4301 > C3 6 15.035 0.0 A 0.374 0.6243 > [ moleculetype ] > ; Name nrexcl > D10 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > 1 C3 1 D10 1C3 1 0.0 15.035 > ; qtot -0.18 > 2 C2 1 D10 1C2 2 0.0 14.027 > ; qtot -0.3 > 3 C2 1 D10 2C2 3 0.0 14.027 > ; qtot -0.42 > 4 C2 1 D10 3C2 4 0.0 14.027 > ; qtot -0.54 > 5 C2 1 D10 4C2 5 0.0 14.027 > ; qtot -0.66 > 6 C2 1 D10 5C2 6 0.0 14.027 > ; qtot -0.78 > 7 C2 1 D10 6C2 7 0.0 14.027 > ; qtot -0.9 > 8 C2 1 D10 7C2 8 0.0 14.027 > ; qtot -1.02 > 9 C2 1 D10 8C2 9 0.0 14.027 > ; qtot -1.14 > 10 C3 1 D10 2C3 10 0.0 15.035 > ; qtot -1.32 > > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 1.530000e-01 5430000 1.530000e-01 5430000 > 2 3 1 1.530000e-01 5430000 1.530000e-01 5430000 > 3 4 1 1.530000e-01 5430000 1.530000e-01 5430000 > 4 5 1 1.530000e-01 5430000 1.530000e-01 5430000 > 5 6 1 1.530000e-01 5430000 1.530000e-01 5430000 > 6 7 1 1.530000e-01 5430000 1.530000e-01 5430000 > 7 8 1 1.530000e-01 5430000 1.530000e-01 5430000 > 8 9 1 1.530000e-01 5430000 1.530000e-01 5430000 > 9 10 1 1.530000e-01 5430000 1.530000e-01 5430000 > > [ pairs ] > ; ai aj funct c0 c1 c2 c3 > 1 4 1 > 2 5 1 > 3 6 1 > 4 7 1 > 5 8 1 > 6 9 1 > 7 10 1 > > [ angles ] > ; ai aj ak funct c0 c1 c2 > c3 > 1 2 3 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 2 3 4 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 3 4 5 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 4 5 6 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 5 6 7 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 6 7 8 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 7 8 9 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > 8 9 10 2 1.110000e+02 4.000000e+02 1.110000e+02 > 4.000000e+02 > > [ dihedrals ] > ; ai aj ak al funct c0 c1 > c2 c3 c4 c5 > 1 2 3 4 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 2 3 4 5 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 3 4 5 6 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 4 5 6 7 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 5 6 7 8 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 6 7 8 9 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > 7 8 9 10 3 0.000000e+00 5.000000e+00 3.000000e+00 > 0.000000e+00 5.000000e+00 3.000000e+00 > > > [system] > sparkling water > [molecules] > D10 208 > > Thank you very much. > > Best Regards, > Kai > -- > 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