[gmx-users] trajconv

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 2 15:15:41 CEST 2007

Hi Ann,

> I run a NPT simulation for 500 picosecond and when i see the output (.gro)
> file in vmd i found some holes my simulation box.
> I mean 2 or 3 chains were away from the center position of the box where
> other chains were residing.
> so i thought of performing a NVT simulation follwed by BD for my system to
> be equillibriated.
> 1. Will that help in the  purpose of equillibriation?

No. This has nothing to do with equilibration but is due to periodic
boundary conditions. Check chapter 3 of the manual, the wiki and the
archives of this list to learn more.

> so, for that i wanted to center all the polymer chains inside the box and
> performed the trjconv program.
> But I wonder
> 2.Which ouput file from my 500 ps simulation (.xtc or .gro )  shall i use to
> perform the trjconv and which options (-pbc nojump, -pbc whole) shall I
> specify inorder to achieve my goal?
> or

For centering you don't need any if the -pbc options. But when using
-pbc nojump you have to make sure that the reference structure is
close to the initial structure in the trajectory you want to reset, as
I explained in more detail last week or the week before.

> 3.the holes that i have mentioned before are accpetable or not?

Not a problem... PBC.

> 4.is it can be the problem with VMD visualisation?

Since it's not a problem it can't be a problem with visualization ;)
(Though it can pose a problem when visualization is the aim, then you
need to use -pbc nojump or inbox)

> out of interest i performed the trjconv with .gro file as follows
> trjconv -f abc.gro -s abc.tpr -pbc nojump -o output.gro
> but when i viewed the output.gro in vmd i found most of my chains were
> broken.

...which is due to a too large shift between the reference structure
(your final structure) and the first structure in your trajectory.

> 5.which file i have to give as input and what makes the difference (.xtc
> file or .gro file?)

Either take the .tpr or take the .pdb file you started from (after
addition of hydrogens and such; the atoms must match).

> then i tried wth .xtc file as input as follows
> trjconv -f abc.xtc -s abc.tpr -pbc nojump -o output.gro
> this time it was not found to be broken.

...which proves my point.

> Waiting for any suggestions

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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