[gmx-users] problem while calculating order parameter

[shakira shukoor]

I guess you have not made your index file correctly. It should contain only
the group for which you will calculate the order parameter.

On Sat, Feb 15, 2020 at 3:21 PM Devargya Chakraborty <
devargyachakraborty.kgp at gmail.com> 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.
>
>  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
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106