[gmx-users] trjconv -pbc nojump across multiple trajectories

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 22 16:08:24 CET 2012

Hi Pablo,

You can use trjcat to stitch the parts of your trajectory together.
A .cpt file contains information about the state, the positions and such.
It doesn't contain static information, like residue/atom names, which are
needed for a reference structure.



On Thu, Nov 22, 2012 at 3:34 PM, Pablo Englebienne <p.englebienne at tudelft.nl
> wrote:

> Hi all,
> I am planning to run a 100ns simulation by continuing a simulation in
> increments of 1ns. After each round, analyses are performed and the
> trajectory scrapped. One of the analysis I need to do is mean square
> displacement; for this I need a continuous trajectory as provided by
> trjconv -pbc nojump.
> The issue that I have is how to make sure that the trajectory stays
> continuous across the different time increments. By reading the manual of
> trjconv, I found out that "the starting configuration for this procedure is
> taken from the structure file, if one is supplied, otherwise it is the
> first frame." I thought of using the .cpt file from the previous step as
> structure file (trjconv -s) for trjconv, but .cpt is not one of the formats
> accepted for that option (only tpr, tpb, tpa, gro, g96, pdb).
> The other issue is that as the dumping of snapshots is performed
> frequently (every 100 timesteps) I would be using double precision, so I
> would like to use a double-precision structure to do the "nojump" step as
> well. A cpt file seems to be perfectly suited for this, as well as a
> single-frame trr file, however neither of them is accepted as a structure
> file for trjconv.
> My questions are 2:
>  1. what would be the best way to ensure a continuous trajectory across
> multiple fragments of a trajectory, using double precision?
>  2. is there a specific reason why a cpt is not accepted as a structure
> file for trjconv -s?
> Thanks for your comments!
> Regards,
> Pablo
> --
> Dr. Pablo Englebienne
> Postdoctoral Researcher
> *TU Delft / 3mE / Process & Energy*
> /Engineering Thermodynamics (ETh) group/
> Building 46
> Leeghwaterstraat 44, room 030
> 2628 CA Delft
> The Netherlands
> *T* +31 (0)15 27 86662 <tel:+31152786662>
> *E* p.englebienne at tudelft.nl <mailto:p.englebienne at tudelft.**nl<p.englebienne at tudelft.nl>
> >
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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