[gmx-users] Running jobs between different Gromacs versions

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 2 22:41:19 CEST 2014

Hey :)

Energy minimization will destroy anything you have for temperature and
pressure and you'll have to re-equilibrate the thermo/barostat. I would say
that a short pre-production run with GMX5 production conditions would be
sufficient (and therefor better) to bring the system from a GMX4 ensemble
to the GMX5 ensemble, just in case there is a small difference between them.

Just my two cents.



On Thu, Oct 2, 2014 at 2:24 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> On 2014-10-02 14:00, Mustafa TEKPINAR wrote:
>> Hi,
>> I was wondering if it is correct to prepare a Gromacs simulation with
>> Gromacs 4.5.5 until production run and to do the production (starting from
>> final tpr file) with Gromacs 5.0.
>> Thanks in advance,
>> Mustafa Tekpinar
>>  Do another minimization with 5.0 before production, then you can say you
> have minimized the starting structure and run production with the same
> software. Be sure to upgrade to 5.0.2!
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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Tsjerk A. Wassenaar, Ph.D.

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