[gmx-users] Precision in trajectory file

[Berk Hess]

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).

Berk

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
format).



Inon.



On 08/03/2010 03:10 PM, Berk Hess wrote:

  Hi,

  

Which program do want to print more digits?

  

PS please don't double post the same question on gmx-developers and
gmx-users.

  

Berk

  

> 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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-- 
Inon Sharony
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