[gmx-users] Retaining only .xtc files and deleting .trr files

[sunita at chem.iitb.ac.in]

Dear Anton,


>> > To be more specific, beside the usage you have specified which other
programs uses only trr file but not xtc file.
>> None. As said, you loose the velocities and in addition you loose
(some)
>> precision on the coordinates. Coordinates in xtc are stored in
>> nanometers with three decimal places. This is sufficient for all kinds
analysis that I am aware of.
>
> thoeretically, you can regenerate the velocities from position + time.
>  and we know
> both precisely so we should be able to recover trr from xtc.
> that's not saying i know how, haven't had to do that yet.
> Kai
>
> On 5/20/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
>> sunita at chem.iitb.ac.in wrote:
>> > Dear Kai,
>> >
>> > Thank you for your response.
>> >
>> > To restart the simulation I can use the last trr file as it contains
velocity term in addition to coordinates. For this purpose I plan to
>> keep
>> > the last trr file. Once I accumulate data for example 50 ns
trajectory
>> and
>> > make xtc file of whole 50 ns, can I delete the trr files?
>> I normaly store them on tape or dvd, then delete them. In addition, I
only write a frame to the trr file every 20-50 ps or so (in stead of 1
or 2 frames per ps for xtc).

As you have mentioned that you write a frame to the trr file every 20-50
ps. What is the frequency generally you take to write velocity to the trr
file.

Can I compare two simulations where in one simulation the frequency to
write velocity is 0.5 ps and in other simulation it is 20 ps. But the
coordinates in the xtc file stored at every 0.5 ps.

Is it going to make any difference?

>> > To be more specific, beside the usage you have specified which other
programs uses only trr file but not xtc file.
>> None. As said, you loose the velocities and in addition you loose
(some)
>> precision on the coordinates. Coordinates in xtc are stored in
>> nanometers with three decimal places. This is sufficient for all kinds
analysis that I am aware of.
>> --
>> Groetjes,
>> Anton
>> * NOTE: New Phone & Fax numbers (below) *
>>   _____________ _______________________________________________________
>> |             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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|_____________|_______________________________________________________|
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>
>
> --
> Kai Zhuang
> BioMedical Engineering @ University of Toronto
> kai dot zhuang at gmail dot com
> kai.zhuang at gmail.com
> 6478314789
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Thanks for any suggestions.
with best regards,
sunita