[gmx-users] g_tcaf use issue

Peter Kroon p.c.kroon at rug.nl
Wed Nov 11 09:33:03 CET 2015

On 11/11/15 03:16, Jones de Andrade wrote:
> Hello.
> We are using gromacs in order to explore how well/not so well different
> methods to calculate dynamical properties of liquids perform.
> At this moment, we are using g_tcaf (already seen g_energy -visc results)
> to evaluate how it would perform in a homogeneous mixture of two organic
> molecules (one with 5 atoms, the other with 19 atoms).
> We are aware of possible convergence and noise issues, so the simulation
> ran for 25 million steps, saved at each 500 (full .trr file). We chose a
> long run + sparse frame recording combination due to disk space limitations.
How long is your simulation in time?
> First thing we noticed, is that -mol flag will lead to a segmentation
> fault. Anyone has any idea on why this?
Try providing a tpr as well with the -s flag. I've seen similar
behaviour in some of the tools in GMX5.
I don't know the answer to the rest of your questions, so I'll them to
the rest of the list.
> Second, without -mol flag, we get results (we tried both with and without
> the -k34 flag), but we are having some difficulties in sorting them out in
> the output files.
> For instance, the *tcaf_all* file show 64 different curves for calculations
> performed without -k34 flag, and 96 with it.I find hard to relate those
> numbers to 3 or 5 (planes), 2 (molecules), 5, 19, 24 (atoms).
> Same problems with the *tcaf_fit* files: 16 curves without -k34 flag, and
> 24 with it.
> The *visc_k* files seems to be more clear: without -k34 flag it yields 4
> "groups of data" (3 planes + 1), while with it I get 6 (5 + 1). Make sense,
> but then again, it seems to "automagicaly" divide the whole simulation in
> time intervals, over which I don't have any control: is that correct? How
> does it choose how to divide it?
> Thanks a lot in advance for anything,
> Jones

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