[gmx-users] Combining .edr-files with eneconv

[Mark Abraham]

Hi,

That all seems very strange. It looks like you're running MPI-enabled
tools, and from your build tree rather than an install tree. Neither of
those uses are encouraged (almost no tools support MPI), though they may
work. I would do a proper install, and configure without MPI, to remove
various potential sources of weirdness there. Please report back what you
see. Using gmxcheck on the -edr files can be a better way to get sanity
feedback than using g_energy.

Mark


On Mon, May 19, 2014 at 10:13 PM, Gmx QA <gmxquestions at gmail.com> wrote:

> Dear users
>
> I have a simulation of a pure popc bilayer for which I am trying to
> calculate the area-per-headgroup for the lipids, simply by using (box_x *
> box_y) / num_lipids
>
> My run is split into different parts, and I was looking at first combining
> the .edr-files with eneconv and then using g_energy to extract the
> box-vectors.
>
> However, when I enter the following:
> $ ~/gromacs-4.6.5/build/src/tools/eneconv_mpi -f prod.part000*edr -o
> prod.edr
>
> I first get this:
>
> Opened prod.part0001.edr as single precision energy file
> Reading energy frame      1 time   20.000
> Opened prod.part0002.edr as single precision energy file
> Energy files don't match, different number of energies:
>  prod.part0001.edr: 52
>  prod.part0002.edr: 52
>
> Continue conversion using only the first 52 terms (n/y)?
>
> This is puzzling, since a "manual" inspection with g_energy of each of
> these two files show the exact same 52 energy terms (and indeed 52==52 :-)
>
> Then web I press y, the following pops up:
>
> Opened prod.part0002.edr as single precision energy file
> Opened prod.part0003.edr as single precision energy file
> Energy files don't match, different number of energies:
>  prod.part0002.edr: 52
>  prod.part0003.edr: 48
>
> Continue conversion using only the first 48 terms (n/y)?
>
> which seems even more strange, since again, using g_energy, there is
> exactly 52 identical energy terms in these two files.
>
> Any ideas about what I am missing, and if should be concerned? Obviously I
> can use g_energy on each .edr-file separately, and the concatenate the
> .xvg-files afterwards, but using eneconv first seems more appropriate
> somehow :-)
>
> Thanks
> /PK
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