AMBER Archive (2009)

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

From: Daniel Roe (droe_at_nist.gov)
Date: Tue Dec 15 2009 - 09:45:20 CST

If you want higher precision trajectories you can use the netcdf
trajectory format (ioutfm=1). The higher precision will likely not
change your results, but netcdf files are more compact and faster to
process than formatted trajectories so it's a good idea to use them anyway.

-Dan

Jason Swails wrote:
> 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!
> Jason
>
> On Tue, Dec 15, 2009 at 3:21 AM, Sidney Elmer <paulymer_at_gmail.com> 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 <case_at_biomaps.rutgers.edu> 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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>
>
>
> 

-- 
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741

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