[gmx-users] problem with trjconv

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Wed Aug 10 16:24:16 CEST 2005

As to my experience, trjconv takes the structure loaded in -s tpr file
as the reference structure, and superimpose the structures in the -f
file to that reference structure. 
So you get the same monomer_2 , because it superimposes monomer_1 in
first.gro to the monomer_1 in the run.tpr. SO nothing changes.

One trick you can play is to exchange 2 monomer order in the -s file,
then fit monomer_2 and output monomer_2.

Or try g_confrms as David suggested.

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Jozef Hritz
Sent: Wednesday, August 10, 2005 10:12 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] problem with trjconv

	Gromacs Users,

I have MD trajectory of protein dimmer. I have observed different
of its monomeric units (they are structuraly identical, composed from
2065 atoms). Therefore I wanted to superimposed the second monomeric
to the first one and then to observe, where are the biggest structural
I have wrote [ monomer_1 ] and [ monomer_2 ] groups with corresponding 
atoms into index.ndx file and then I had run trjconv

For the initial structure:
trjconv -f first.gro -o monomer_2.gro -s run.tpr -n index.ndx -fit

For least squares fit I have used group [ monomer_1 ] and for output
[ monomer_2 ]. When I have checked the output, there was no fit done. It
just took monomer_2 part from initial structure first.gro without

In the second step I wanted to fit monomer_2 part to monomer_1 during
whole MD trajectory, but as I wrote I have even problem with the first

Can anybody help me with this problem?  

Thank You

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