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

Mark Abraham mark.j.abraham at gmail.com
Mon Sep 3 05:07:35 CEST 2018


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.


On Mon, Sep 3, 2018 at 2:11 AM Stephani Macalino <stephanimacalino at gmail.com>

> 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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