Thanks a lot for the replies..now everything is clearer.
Just another question..which is at the basis of all the problem
ascii/bin trajectories I submitted to the forum.
I need to map exactly the coordinates to the velocities for each frame
(I have to run new simulations - with different parameters - starting
from "hot" frames, that have given structural patterns, and study the
time decay of such patterns eith shorter timesteps).
I intended to do it with ptraj, dumping coordinates (from mdcrd) and
velocities (from mdvel) and then combining them into hot restart
files. But from the tests I made, it seemed as if the netcdf velocity
trajectory cannot be read by ptraj:
>NETCDF file:
>Error: No coordinates are present in the NetCDF file md19_bin.mdvel
>Error setting up NETCDF trajectory for reading.
That's why I tried formatted trajectories, and wanted to verify if the
two types of trajectories were consistent.
So I think that the best I can do now is to save formatted
trajectories (coordinates and velocities), perform the structural
analysis and save the frames I need. What do you think?
Thanks again
Lorenzo
2011/6/1 Jason Swails <jason.swails.gmail.com>:
> On Wed, Jun 1, 2011 at 6:11 AM, Lorenzo Gontrani <l.gontrani.caspur.it>wrote:
>
>> Dear all, here it is the output of a ptraj dihedral analysis on the same
>> system, for both ASCII and BINARY trajectory. Starting from frame 14,
>> the values start to diverge significantly.
>>
>
> I don't understand what you're doing here. Is the ASCII trajectory the
> *same* as the NetCDF trajectory? Were they from 2 different simulations?
> Or were they from the same simulation? If they were from the same
> simulation, what was the original format (NetCDF or ASCII)?
>
> That said, Binary trajectories have much higher precision, so the actual
> values of the coordinates are in fact different between binary and ASCII
> (since ASCII truncates to 3 decimal places). Inserting this loss of
> precision into a dihedral calculation could lead to the results you're
> seeing here.
>
> If they're actually 2 separate simulations, then there's no reason to expect
> them to be identical, as machine-precision limits reproducibility,
> *especially* across non-identical hardware. In fact, probably the *only*
> way to ensure reproducibility is to use the GPU code, which is completely
> deterministic.
>
> HTH,
> Jason
>
>
>> BINARY ASCII
>>
>> 1.00 -147.958668 | 1.00 -147.942612
>> 2.00 -72.048594 | 2.00 -72.067980
>> 3.00 18.534202 | 3.00 18.516501
>> 4.00 82.936517 | 4.00 82.915310
>> 5.00 141.777751 | 5.00 141.796965
>> 6.00 26.969903 | 6.00 26.895879
>> 7.00 -67.860564 | 7.00 -67.880553
>> 8.00 -130.117973 | 8.00 -130.058275
>> 9.00 -83.235696 | 9.00 -83.207713
>> 10.00 -44.748722 | 10.00 -44.763429
>> 11.00 -134.239920 | 11.00 -134.211415
>> 12.00 -135.534592 | 12.00 -135.964199
>> 13.00 -120.563889 | 13.00 -120.421923
>> 14.00 148.857056 | 14.00 155.068374
>> 15.00 145.166697 | 15.00 179.217652
>> 16.00 123.163784 | 16.00 -127.158826
>> 17.00 163.278049 | 17.00 -127.651488
>> 18.00 169.775862 | 18.00 -116.616523
>> 19.00 170.453577 | 19.00 -118.063325
>> 20.00 -168.840722 | 20.00 -146.686249
>>
>> I hope that someone can help someway..
>>
>> Lorenzo
>>
>> --
>> =======================================
>> Lorenzo Gontrani
>> Research associate of EDXD group
>> University of Rome "La Sapienza"
>>
>> GSM +39 338 7615798
>> WORK +39 06 49693273
>> Email l DOT gontrani AT caspur DOT it
>> Webpage: http://webcaminiti/gontrani.html
>> =======================================
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
=======================================
Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
=======================================
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Received on Wed Jun 01 2011 - 09:00:03 PDT
