[gmx-users] TPIC and GMX_TPI_DUMP

João M. Damas jmdamas at itqb.unl.pt
Sat Aug 31 02:19:49 CEST 2013

PBC is on works, so the centering is not important. My question had to do
with the center of insertion: random for tpi, specific for tpic.

That's really my second guess, the infinite energies. The tpi code has a
way to deal with them internally. Run the insertion [mdrun] with "-debug 1"
flag and see how many non-finite energies do you hit. Maybe all (number of
frames times the number of insertions?

Can you post 100 lines or so of your .xvg file? I'm curious about it. Maybe
4.6.3 has some new output I'm unaware of.

Also, can you tell something more about your system?


On Sat, Aug 31, 2013 at 12:55 AM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:

> Thanks for the reply João,
> I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
> group.
> I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
> single .pdb file written.
> I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per
> frame. I think it may have to do with the frames that have infinite
> chemical potential with the insertion? It doesnt seem to have anything to
> do with TPI_DUMP, when I lower rtpi to 0.05 the .xvg file becomes less
> ridiculously large, only 0.5 gigs...
> I suppose I need to try an older version of gromacs, and see if my setup
> works there
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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