[gmx-users] Topology file and itp file

[lan hoa Trinh]

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.abraham at gmail.com>:

> Hi,
>
> How are you assessing "different?"
>
> Mark
>
> On Thu, 20 Apr 2017 21:13 lan hoa Trinh <trinhlanhoa at 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*
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