[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 17 20:50:02 CET 2014

Hi Andrew,

You can convert each frame to trr and concatenate those.


On Mar 17, 2014 8:18 PM, "Andrew DeYoung" <adeyoung at andrew.cmu.edu> wrote:

> Hi,
> I have been creating several .g96 configuration files "by hand" (actually,
> using a scripting language).
> I like .g96 as a configuration file format because it provides 9 decimal
> places of precision for the x, y, and z coordinates of the position and
> velocity of atoms in my system -- whereas .gro and .pdb configuration file
> formats offer much lower precision.  My system is crystalline, and I found
> many months ago that the lower precision offered by .gro and .pdb is not
> quite enough to achieve the exact bond lengths that I want in my crystal.
> Many months ago, Professor van der Spoel suggested on this list that I
> switch to .g96 for my configurations.
> So for many months I have been successfully using .g96 configurations as
> input to grompp to make the .tpr files necessary for simulation.
> Today, however, I am trying to do something somewhat unusual, and I run
> into
> an unusual problem.  Suppose I have made three .g96 configurations "by
> hand": conf1.g96, conf2.g96, and conf3.g96.  I want to compute the
> single-point energy of all three configurations.
> (Why would I want to do this?  I have written code in a scripting language
> to generate frames in which a particular angle is "scanned" from one
> extreme
> to the other; I want to use Gromacs to simply compute the single-point
> energy at each frame in the "scan," without taking any MD moves.)
> One way to do this might be to run three different zero-step MD
> simulations,
> by passing the three configurations separately to grompp, obtaining three
> separate .tpr files, and passing those three .tpr files to mdrun.  But this
> documentation page
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> warns that zero-step MD simulations have "complications related to catering
> to possible restarts" and is not recommended.  Doing it that way is also a
> little inconvenient because eventually I will have dozens or hundreds of
> separate "handmade" .g96 configurations for which to calculate the
> single-point energy, and running hundreds of zero-step simulations would
> probably require some sort of bash script.
> So, my thought is to concatenate the three (or more) .g96 configurations
> into a single trajectory, and then feed that trajectory to the -rerun
> switch
> of mdrun to compute the energy of each frame.
> My question is, how can I concatenate three (or more) .g96 configurations
> into a single trajectory of any type?
> I have tried:
> trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr
> But I get this error message:
> -------------------------------------------------------
> Program trjcat, VERSION 4.5.5
> Source code file: trxio.c, line: 693
> Fatal error:
> Reading trajectories in .g96 format is broken. Please use
> a different file format.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Reading trajectories in .g96 format may be broken, but reading
> CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass
> g96
> configurations to the -c switch of grompp).
> Is there any other way I can concatenate three (or more) .g96
> configurations
> into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going
> through .gro or .pdb (e.g., by converting from .g96 using editconf), which
> have lower precision?
> Thanks so much for your time!
> Andrew DeYoung
> Carnegie Mellon University
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