[gmx-users] Position restraints problem

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 30 11:33:04 CEST 2012

Hey :)

A sed oneliner to generate position_restraints for the first
moleculetype in a file, using an fc of 200:

sed -n -e '/\[ *atoms *\]/,/^ *\[/{/^\( *[0-9]\+\) .*/s//\1 1 200 200
200/p}' -e '/\[ *atoms *\]/i[ position_restraints ]' molecule.itp



On Wed, Mar 28, 2012 at 3:33 PM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> True. Even more so if the position restraints file can be generated with basic Bash commands in under a minute.
> Jernej
> On 28. mar. 2012, at 20:16, gmx-users-request at gromacs.org wrote:
>> It's pretty rare to have more than a handful of [moleculetype] sections,
>> each of which would want customized [position_restraints]. pdb2gmx will
>> write all-heavy-atom [position_restraints] sections which serve most
>> purposes. It would not be hard to modify genrestr to be useful in the
>> general case, but until a developer needs it badly enough, it'll be a
>> low priority :-)
>> Mark
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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