[gmx-users] g_trjorder output

Apramita Chand apramita.chand at gmail.com
Wed Jun 6 11:47:04 CEST 2018

 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?

Yours sincerely,
Apramita Chand

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