[gmx-users] Precision in trajectory file
gmx3 at hotmail.com
Tue Aug 3 14:39:38 CEST 2010
No, the program is not mdrun.
mdrun writes a trr file will full precision binary x, v and f.
You can use another tool on this output trr to print the information.
There is gmxdump which does a dump (not full double precision currently) in an incovenient format.
I guess trjconv would be the most convenient program, it currently supports many output formats
but none with more than 9 decimals (g96 has the most decimals, I believe).
Date: Tue, 3 Aug 2010 15:29:32 +0300
From: InonShar at TAU.ac.IL
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Precision in trajectory file
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
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
> format. Otherwise, it cannot be recognized by other softwares,
> For the .trr files, I guess, if you are indeed running
> GMX, the leap-frog integrator is using double-precision
> the printed value in .trr is also truncated due to the format
> 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
> > 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
> > single-precision as 0.000 nm, and in double-precision as
> > Since I've already spent computation time at getting
> > I'd like to make use of all of it -- for my own reasons. I
> > searched the manuals, mailing lists and source code for
> > but didn't find any.
> > Could you please tell me how I can change the number of
> > out (e.g. to the .trr file)? I'm looking for a more elegant
> > than adding a printf line to the source code. Something along
> > lines of changing the format of numbers in the function that
> > .trr .
> > Thanks in advance!
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