[gmx-users] Doubts in g_select and g_trjconv

Apramita Chand apramita.chand at gmail.com
Tue Jun 5 21:02:09 CEST 2018

With reference to my earlier message, I have also 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 moelcules.

But when I add -com option, all of the numebrs decrease to 0 or 1.

So is it wrong to add -com option? Considering we're already specifying -da
as 0?

Yours sincerely,
Apramita Chand

From: Apramita Chand <apramita.chand at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] Doubts regarding g_select
        <CA+gTzoZReWmzJhKH4tmPwHA12WqR5OB0Y_BU_w8fh16oQD3DZA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

 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

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,

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,

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