[gmx-users] Doubts regarding g_select

[Apramita Chand]

 Dear All,
I am confused between different commands and their outputs for g_select. 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.
I have a total of 18 urea molecules in my system

One of the commands:
g_select -select ' resname UREA and within 0.45 of group Backbone' -f
100nc_entire.xtc -s md.tpr -os size_within0.45_urea_backbone.xvg -oi
index_within0.45_urea_backbone.dat -oc cfrac_urea_within0.45_backbone.xvg
-seltype mol_com

gives 6,5,4,3...etc urea molecules in the size.xvg file which seems to be
correct

But if I give the same command by changing it to
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'

I get 0 or 1 urea molecule for every time frame.


Again, I want to generate no.of urea molecules beyond 0.45,

Giving,
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'
I get all 18 urea molecules in the above 0.45 regime


That is confusing!

I think the first command that specified within 0.45 nm is correct for my
system and I would like a similar command that can specify beyond 0.45nm.

This problem persists even when I increase urea molecules to 40 or 80.
THere's just 1 molecule below 0.45nm and all of the others above 0.45nm.
But the hydrogen bond numbers show increasing no. of hydrogen bonds between
peptide-urea (increases upto 6-9) . What could be going wrong?

Any suggestions regarding this problem?


Yours sincerely,
Apramita