[gmx-users] problem while calculating order parameter

[Devargya Chakraborty]

Thanks

On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/20 4:50 AM, Devargya Chakraborty wrote:
> > i want to calculate the order prameter between two carbon atom namrd C01
> > and C03 in my topology file but while calculating, i am getting the
> > following error.
>
> gmx order is designed to compute deuterium order parameters in alkyl
> chains. It requires special index groups that only contain the atoms of
> interest and those flanking them to define the local molecular axis. See
> http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an
> example.
>
> -Justin
>
> >   Taking z axis as normal to the membrane
> > Reading file nvt.tpr, VERSION 2019.1 (single precision)
> > Using following groups:
> > Groupname: System First atomname: C01 First atomnr 0
> > Groupname: Other First atomname: C01 First atomnr 0
> > Groupname: EMI First atomname: C01 First atomnr 0
> > Groupname: NSC First atomname: NBT First atomnr 760
> > Groupname: Water First atomname: OW First atomnr 1360
> > Groupname: SOL First atomname: OW First atomnr 1360
> > Groupname: non-Water First atomname: C01 First atomnr 0
> > Groupname: C01 First atomname: C01 First atomnr 0
> > Groupname: C04 First atomname: C04 First atomnr 1
> > Groupname: C03 First atomname: C03 First atomnr 2
> > Groupname: H07 First atomname: H07 First atomnr 3
> > Groupname: H09 First atomname: H09 First atomnr 4
> > Groupname: H08 First atomname: H08 First atomnr 5
> > Groupname: C05 First atomname: C05 First atomnr 6
> > Groupname: H0B First atomname: H0B First atomnr 7
> > Groupname: H0C First atomname: H0C First atomnr 8
> > Groupname: H0D First atomname: H0D First atomnr 9
> > Groupname: N00 First atomname: N00 First atomnr 10
> > Groupname: C06 First atomname: C06 First atomnr 11
> > Groupname: H0F First atomname: H0F First atomnr 12
> > Groupname: C0N First atomname: C0N First atomnr 13
> > Groupname: H0O First atomname: H0O First atomnr 14
> > Groupname: H0P First atomname: H0P First atomnr 15
> > Groupname: H0Q First atomname: H0Q First atomnr 16
> > Groupname: N02 First atomname: N02 First atomnr 17
> > Groupname: H0E First atomname: H0E First atomnr 18
> > Groupname: NBT First atomname: NBT First atomnr 760
> > Groupname: SBT First atomname: SBT First atomnr 761
> > Groupname: OBT First atomname: OBT First atomnr 763
> > Groupname: CBT First atomname: CBT First atomnr 764
> > Groupname: F1 First atomname: F1 First atomnr 768
> >
> > Reading frame       0 time    0.000   Number of elements in first group:
> > 10360
> >
> > -------------------------------------------------------
> > Program:     gmx order, version 2019.1
> > Source file: src/gromacs/gmxana/gmx_order.cpp (line 546)
> >
> > Fatal error:
> > grp 1 does not have same number of elements as grp 1
> >
> > can anybody help.
> >
> > Thanks
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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