[gmx-users] Precision in trajectory file
InonShar at TAU.ac.IL
Tue Aug 3 14:29:32 CEST 2010
Thanks for both replies.
I would like the trajectory information (i.e. positions and velocities)
as well as forces (which, as I understand it, can also be printed to the
same trajectory file) to be output with a larger (user defined?)
precision. I think the "program" which should do this is mdrun.
I also noticed a function call for "write_traj" in the /src/kernel/md.c
file. I also looked in static.c as well as trnio.c and could not find
what I was looking for (an fprintf line which prints formated
coordinates to trajectory file, and specifies the precision of that format).
On 08/03/2010 03:10 PM, Berk Hess wrote:
> Which program do want to print more digits?
> PS please don't double post the same question on gmx-developers and
> > Date: Tue, 3 Aug 2010 13:26:44 +0200
> > From: qiaobf at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Precision in trajectory file
> > The number of digits in .gro( or .pdb) is crudely fixed because of the
> > format. Otherwise, it cannot be recognized by other softwares, like VMD.
> > For the .trr files, I guess, if you are indeed running double-precision
> > GMX, the leap-frog integrator is using double-precision coordinates, but
> > the printed value in .trr is also truncated due to the format problem.
> > Inon Sharony wrote:
> > > Good afternoon!
> > >
> > > It seems to me that although I'm running a double-precision
> > > installation of GROMACS, the printout to file (of the positions and
> > > velocities) is of much less precision. i.e. the computation is done on
> > > numbers with something like 16 significant digits, but the last 10 of
> > > those are simply truncated and lost (e.g. positions are given in
> > > single-precision as 0.000 nm, and in double-precision as 0.00000 nm).
> > > Since I've already spent computation time at getting double-precision,
> > > I'd like to make use of all of it -- for my own reasons. I already
> > > searched the manuals, mailing lists and source code for instruction
> > > but didn't find any.
> > > Could you please tell me how I can change the number of digits printed
> > > out (e.g. to the .trr file)? I'm looking for a more elegant solution
> > > than adding a printf line to the source code. Something along the
> > > lines of changing the format of numbers in the function that prints to
> > > .trr .
> > >
> > > Thanks in advance!
> > >
> > --
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