[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?
adeyoung at andrew.cmu.edu
Mon Mar 17 20:11:56 CET 2014
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
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
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!
Carnegie Mellon University
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