[gmx-users] g_trjorder output

Justin Lemkul jalemkul at vt.edu
Wed Jun 6 15:30:08 CEST 2018

On 6/6/18 5:47 AM, Apramita Chand wrote:
>   Dear All,
> I want to choose a cutoff of 0.45nm and want to calculate the no. of urea
> molecules within 0.45 as well as beyond 0.45nm of the peptide backbone(for
> calculation of preferential interaction coefficient)
> I have a total of 18 urea molecules in my system.
> I have tried the g_trjorder command giving reference group as Backbone.
> When I give the command,
> g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45
> -da 0
> I am getting reasonable no.of urea molecules like 6,8,9,etc.  Same goes for
> water molecules.
> But when I add -com option, all of the numbers decrease to 0 or 1. The
> problem persists even on increasing the no. of urea molecules to 40 or 80.
> So is it wrong to add -com option? Considering we're already specifying -da
> as 0?

It is very unlikely that many molecules satisfy a COM distance cutoff of 
0.45 nm. Whereas that is a suitable cutoff for atom-atom distance, using 
the COM as the metric will require a different value.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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