[gmx-users] Gro file does not match topology file... continue

[Mark Abraham]

Hi,

That's impossible. The error here is that things do not match. You can't
get it if things match, as you claim ;-) But if you can reproduce it,
please file a bug.

On Poncho's case - as Justin says, count atoms in molecules and numbers of
molecules and find out what doesn't match what you think is there. A
difference of 8 atoms obviously can't be solely due to wrong count of
three-atom solvent molecules.

Mark

On Fri, 27 Jan 2017 18:58 Tasneem Kausar <tasneemkausar12 at gmail.com> wrote:

> I was having the same problem. The atoms in topology and gro were same and
> this error was there. By increasing box size the problem was resolved.
> What would be tge reason for that.?
>
> On 27 Jan 2017 22:30, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/27/17 11:48 AM, Tasneem Kausar wrote:
> >
> >> Increase your box size.
> >>
> >>
> > Changing the box will not solve this issue.  If you make a mismatched
> > system bigger, it's still mismatched.
> >
> > -Justin
> >
> > On 27 Jan 2017 22:15, "Poncho Arvayo Zatarain" <poncho_8629 at hotmail.com>
> >> wrote:
> >>
> >>
> >>>
> >>> Hello: according to the queshere abouttion and the answer send me here
> >>> about gro (58674) file does not mtch with the topology (58666), i
> checked
> >>> my gro file at the top corner on the left and said 58674, and at the
> end
> >>> of
> >>> the file the number of molecules is the same, 58674. i used TIP3 model
> >>> and
> >>> 2 phospholipids: 26 dppe and 230 dppe also 8960 of TIP3.
> >>> My top file is
> >>> : Include forcefield parameters
> >>> #include "toppar/charmm36.itp"
> >>> #include "toppar/compound.itp"
> >>> #include "toppar/DPPC.itp"
> >>> #include "toppar/DPPE.itp"
> >>> #include "toppar/TIP3.itp"
> >>>
> >>> [System]
> >>> : Name
> >>> Title
> >>>
> >>> [Molecules]
> >>> : Compound #mols
> >>> COMPOUND    72
> >>> DPPE                230
> >>> DPPC                26
> >>> TIP3                  8960
> >>> --
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> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
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