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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
