Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance, Best regards,
*Lan Hoa* 2017-04-20 14:25 GMT-05:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > How are you assessing "different?" > > Mark > > On Thu, 20 Apr 2017 21:13 lan hoa Trinh <trinhlan...@gmail.com> wrote: > > > Dear All, > > I am modelling a system of spherical beads (which I named as Fi) which > only > > repulsive each other. I would highly appreciate if some one can have a > look > > at the following topology which I created: > > (ficoll1.top) > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > > 1 1 no > > > > > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.000 0.000 A 0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; name number > > Ficoll 64 > > > > I also created another topology: > > (ficoll2.top) > > > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > > 1 1 no > > > > #include "fi.itp" > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; name number > > Ficoll 64 > > > > where fi.itp is the following: > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.000 0.000 A 0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > I expected that the simulation with the 2 topology files should gave the > > same results but they gave the different results, > > > > I don't understand what is wrong here. > > Thank you very much in advance. > > Best regards, > > *Lan Hoa* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.