[gmx-users] problem while calculating order parameter

[Justin Lemkul]

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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