[gmx-users] Combining edr files for NPT with different dt values

[Stephani Macalino]

Hello,
Thanks for your prompt response!
I am doing this since I am following the gromacs tutorial of checking the
pressure and density stabilization of my system (I'm a newbie).
I just found one instruction where it mentioned about doing interactive
commands (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-April/060733.html
),
i.e. using a .txt file with 'c' for each line (depending on the number of
edr files) and -settime as you have mentioned.
This solution has worked for me.
Thanks again!
Regards,
Stephani

On Mon, 3 Sep 2018 at 12:08, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> You'll have to look more closely at the way you tried to concatenate them
> and see why the file you eventually gave to gmx energy had only 2ns. For
> example, if each check treated its first step as time zero, then you need
> to consider gmx eneconv -settime, etc. But I wouldn't bother with any of
> this for equilibration. If the last segment is consistent with the ensemble
> you seek, then that is the job done.
>
> Mark
>
> On Mon, Sep 3, 2018 at 2:11 AM Stephani Macalino <
> stephanimacalino at gmail.com>
> wrote:
>
> > Hello,
> > I am trying to combine edr files using the gmx eneconv command.
> > I did 6 cycles of equilibration (1 NVT and 5 NPT). The NPT cycles are 2ns
> > each but the first 2 have a dt of 0.001 while the last 4 have dt of
> 0.002.
> > I tried to combine them and check the density using gmx energy command
> but
> > I keep getting a file with only 2ns of time included, when it should be
> > 10ns.
> > I thought maybe because the dt is different, but when I only combined the
> > first 2, I still only got 2ns instead of 4ns.
> > All other parameters are the same for the mdp files of each equilibration
> > cycle. The only difference are the dt and force constants used.
> > How can I combine these files so I can analyze my pressure and density
> > graphs?
> > Hope you can help.
> > Thank you!
> > Regards,
> > Stephani
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