[gmx-users] TPIC and GMX_TPI_DUMP

João M. Damas jmdamas at itqb.unl.pt
Fri Aug 30 23:51:14 CEST 2013

Dear Rafael,

Which version of GROMACS are you using? I cannot guarantee my following
comments are valid in 4.6.X, only on 4.0.X and 4.5.X.

What values have you tried from GMX_TPI_DUMP? Basically, the value you set
it to will be the energy value that will be compared with the epot of the
system with the molecule inserted. Intuitively, I think you're choosing
very low values for GMX_TPI_DUMP, as probably the insertion of the water
molecule is mostly unfavorable, and the epot is, therefore, hugely large.
I'd suggest GMX_TPI_DUMP=1e+20 for a start (be careful, you *will* get a
lot of .pdb files: try inserting on a single trajectory frame as a test
case and reducing the number of insertions [nsteps]).

I don't understand why is your .xvg getting that big, unless you're using a
huge trajectory. In tpi(c).xvg, you only have one line per ps, and the
GMX_TPI_DUMP doesn't increase the output to the .xvg, IIRC.

On another note, I hope you're using the tpic algorithm, with the center of
insertion set to the geometric center of your prosthetic group, and not the
tpi algorithm.

I hope this helps.


On Fri, Aug 30, 2013 at 8:16 PM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:

> Hi all,
> I am trying to insert a water into a prosthetic group binding cavity. I
> cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP
> in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I
> cant really get good information out of the .xvg output either, it always
> ends up being like 2+ gigs, and is basically unreadable, plus, writing this
> file takes a long time, and gums up the processors.
> So 2 questions, can I suppress the writing of the .xvg file, and how do I
> get GMX_TPI_DUMP set correctly?
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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