[gmx-users] g_tcaf use issue
Jones de Andrade
johannesrs at gmail.com
Thu Nov 12 02:52:52 CET 2015
Sorry for the delay in answering you. Long day. ;)
On Wed, Nov 11, 2015 at 5:32 AM, Peter Kroon <p.c.kroon at rug.nl> wrote:
> 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
> > 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
> How long is your simulation in time?
25 million steps of one femtosecond each, so it is 25ns of simulation.
> > 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.
Unfortunately, it is on our command line: -s *.tpr file is in there. So, it
is not that file lacking that is the root for this issue. :(
> I don't know the answer to the rest of your questions, so I'll them to
> the rest of the list.
Thanks for the help anyway. Anybody else has any ideas? Shouldn't
*tcaf_fit* files have 6 curves without -k34 flag and 10 with it, as opposed
to 16 and 24 respectively I'm getting?
Also, how does g_tcaf program (automatically) divides the trajectory frames
to get the data provided in the *visc_k* files?
Thanks a lot!
> > Second, without -mol flag, we get results (we tried both with and
> > the -k34 flag), but we are having some difficulties in sorting them out
> > the output files.
> > For instance, the *tcaf_all* file show 64 different curves for
> > 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,
> > 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
> > but then again, it seems to "automagicaly" divide the whole simulation
> > time intervals, over which I don't have any control: is that correct?
> > does it choose how to divide it?
> > Thanks a lot in advance for anything,
> > Jones
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