Re: [AMBER] comparing coordinates from restart file and ptraj outputs

From: Jason Swails <>
Date: Tue, 15 Dec 2009 07:00:41 -0500

The problem is not with the mdcrd precision, it is the fact that the
time step of the restart file is one greater than the time step of the
final frame in the mdcrd file. The trajectory file should have 3
decimal places in each coordinate (unless maybe your coordinates have
absolute values > 1000? This would most likely not happen if you use
iwrap=1 for your MD simulations) which should provide plenty of
resolution for its intended usage (see Professor Case's description).
Properties derived from the mdcrd will not be that sensitive to
changes in only the 4th decimal place for each coordinate, so the
existing precision is fine for that use. Restart files have a greater
precision since they're used to restart simulations.

Thus, I'd suggest that you leave the mdcrd format intact, though if
you were really intent on changing this it would have to be done in
the source code (you'd have to find the appropriate format statement
that the mdcrd file uses for its output and change it to include more
decimal places).

However, the existing tools used to analyze trajectories (ptraj, or
sander if you're using imin=5) may expect to see the default format,
so you would have to either change these programs to read your new
format, or write your own analysis scripts/programs. In any case, it
seems a daunting task for so little gain (if any gain is to be made,
which I'm doubtful of).

Good luck!

On Tue, Dec 15, 2009 at 3:21 AM, Sidney Elmer <> wrote:
> I realized that the problem was with the precision of the mdcrd coordinates,
> which is 2 decimal places.  Is there any way to increase the precision of
> formatted trajectory files?  Two decimal places is too low resolution.
> Thanks.
> Sid
> On Mon, Dec 14, 2009 at 7:28 PM, case <> wrote:
>> On Mon, Dec 14, 2009, Sidney Elmer wrote:
>> >
>> > 3. thus, after execution finishes, the coordinates in "restrt" file
>> should
>> > match coordinates from frame 500, correct?
>> No.  The coordinates stored in the restart file are one time step ahead
>> of the last snapshot in the trajectory file.  Restart files should be used
>> for exactly that: restarting an existing trajectory.  Trajectory files
>> should
>> be used for sampling the coordinates traversed by the simulation.
>> ...dac
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Dec 15 2009 - 04:30:02 PST
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