[gmx-users] problem with topology

[Dallas Warren]

The fact that you have separate, exactly defined molecules, you are
far better off running x2top with a single molecule, take the .top it
generates and convert it to an .itp file. Then use that for your
multiple molecule system.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 11 Jun 2019 at 21:29, Maria Luisa <ml.perrotta at itm.cnr.it> wrote:
>
> Thank you for your rapid answer.
> 1- No I haven't an itp for each molecule. I wrote opls atomtypes on n2t
> files that is in oplsaa.ff directory.
> 2- To generate the box with the two kind of molecules I used the gmx
> insert-molecules command. Ar first I inserted 100 molecules of PVDF and
> then the 1436 molecules of ATBC, setting box size at 15x15x15nm (x,y and
> z). Then I wanted a smaller box size (in particular 10.2x10.2x10.2) and so
> I used the command gmx editconf , in particular
>
> gmx editconf -f oldbox.gro -o newbox.gro -box 10.2 10.2 10.2 -density 1000
> It because I want a density of the system equal to 1 g/ml. I think that
> the problem is in this stage, because if I compare the oldbox.gro and the
> newbox.gro trough using of VMD I see differents bond from molecules, and I
> think that they interact.So in this case the system is not able to
> recognize these bonds.
>
> Anyway the exact command that I used to create topology is:
>
> gmx x2top -f newbox.gro -o topol.top -ff oplsaa
>
>
>
>
> > Do you have a .itp for each molecule? How did you generate the box with
> > the
> > multiple molecules? What is the contents of your .top file? What was the
> > exact commands you used? What was the exact output? Copy and paste, do not
> > type out what you think it says.
> >
> > Suspect there may be a problem with how you are calling the topology.
> >
> > On Tue, 11 Jun. 2019, 6:32 pm Maria Luisa, <ml.perrotta at itm.cnr.it> wrote:
> >
> >> Dear user.
> >> I have a problem. I have to simulate a box of 100 molecules of
> >> polyvinylidene fluoride (PVDF) and 1436 molecules of the solvent ATBC.
> >> At
> >> first I built the single chain of PVDf and a single molecules of ATBC,
> >> and
> >> I was able to construct topology using opls force-field. The command
> >> that
> >> I used is gmx x2top. When I create the complete box with a total amount
> >> of
> >> 95320 atoms, an error occurs saying to me that it's possible recognize
> >> only 1800 atoms of 95320. This is strange, because the two molecules are
> >> written in the topology file each one, but not together in the box. What
> >> is the problem? Is there some bug with my version of gromacs (5.1.4)?
> >>
> >> I wait for your answer
> >> Maria Luisa
> >>
> >>
> >> Maria Luisa Perrotta
> >> Ph.D Student, CNR-ITM
> >> via P.Bucci, 87036 Rende (Cs)
> >> Italy
> >> email: ml.perrotta at itm.cnr.it
> >>
> >>
> >> --
> >> 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-request at 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-request at gromacs.org.
> >
>
>
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perrotta at itm.cnr.it
>
>
> --
> 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-request at gromacs.org.