[gmx-users] how can I exclude the solvent from the output?

[Mark Abraham]

Hi,

That doesn't apply to an energy minimization, which rarely writes enough
output to care about at all. xtc-grps are active for the other kinds of
integrators in mdrun.

Mark


On Tue, Jan 28, 2014 at 6:13 PM, Athina Meletiou
<enxam16 at nottingham.ac.uk>wrote:

> Hello!
>
> I am interested in running a simulation of a mycolic acid; the solvent is
> water.
>
> However, I need to exclude the solvent from being written in the output in
> order to reduce the data volume.
>
> So, after using editconf and genbox, what I did was edit the mdp file and
> add the following lines on the 'output control options' section:
>
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps                 = MEO
> ; Selection of energy groups
> energygrps               = MEO
>
>
> I ran grompp using the input as described above. Then I did an energy
> minimization with mdrun, but the output I got still contains the solvent.
>
> So obviously I did something wrong. Unfortunately searching the web didn't
> provide me with any answers, I know I need to edit the lines mentioned
> above but I am not sure how to actually edit them.
>
> Thank you so much in advance!
>
> Best regards
> Athina
>
>
> Athina Meletiou
> Department of Chemical and Environmental Engineering
> University of Nottingham
> University Park
> NG7 2RD
> Email: enxam16 at nottingham.ac.uk<mailto:enxam16 at nottingham.ac.uk>
>
>
>
>
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