[gmx-users] energy minimization

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Sep 28 11:27:57 CEST 2016

Hi Surya,

I'm not sure I understand what you want to do.
Do you want to energy minimise an entire trajectory? After the production
phase? Why?

The -c flag in mdrun is the output, the last conformation sampled during
the mdrun. You can use this output file as the input structure for an
energy minimisation (-c option in grompp to prepare the .tpr file), I just
don't see the point in doing that.
Also, -c flag in grompp doesn't accept .xtc files. If you type "grompp -h"
you'll see that.


On 28 September 2016 at 05:53, Seera Suryanarayana <palusoori at gmail.com>

> Dear gromacs users,
> I have done simulations for 100ns. I would like to do energy minimization
> by using trajectory file which I got after production phase. Can I do
> energy minimization passing the trajectory file to -c argument? If it is
> yes, then tell me how to do it.
> Thanks in advance
> Surya
> Graduate student
> India.
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Catarina A. Carvalheda

PhD Student
Computational Biology Division
University of Dundee
DD1 5EH, Dundee, Scotland, UK

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