[gmx-users] VMD and trajectory files

[Martina Bertsch, PhD]

Dear Derrick,


According to the GROMACS manual, the xtc format is a compressed, 
portable format for trajectories, containing only coordinates, while trr 
is a binary, full precision file, containing x, v and f information. The 
xtc uses the xdr routines for writing and reading data which was created 
for the Unix NFS system. The trajectories are written using a reduced 
precision algorithm which works in the following way: the coordinates 
(in nm) are multiplied by a scale factor, typically 1000, so that you 
have coordinates in pm. These are rounded to integer values. Then 
several other tricks are performed, for instance making use of the fact 
that atoms close in sequence are usually close in space too (e.g. a 
water molecule). To this end, the xdr library is extended with a special 
routine to write 3-D float coordinates.

I think that since xtc files contain only coordinates and are therefore 
significantly smaller, they might be more suitable for import into VMD. 
Here is what Anton said about writing out xtc and trr trajectories:

"I use the default ndec=3, that is sufficient for all types of analysis that I ever heard of. I tune nstxout/nstvout so that a frame is written
to .trr file every few hours along the calculation (usually every 10-50ps). Depending on how much disk is on the machine I run on, I either write the whole system to .xtc every 1 ps, or I only write protein(s) + substrate(s) + co-factor(s). That, I also put on CD (or, recently, on DVD!). Then, I make one .xtc file with only the 'protein+stuff' in it (if I haven't got that
already), and a few ones with less frames, like every 10 ps and every 100ps, which I can use for quick analysis (e.g. an rmsd plot)."

Greetings,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611

Ilya Chorny wrote:

>I'm not exactly sure what the advantage is to using the xtc vs trr. I
>think both will work. I believe the trr output can be adjusted by
>setting nstxout = 100. The trr files contains more info then just
>coordinates like velocities and forces.
>
>-x option in mdrun directs the output to a file name for the .xtc
>output.
>
>type mdrun -h for more info 
>
>Ilya
>
>
> 
>On Thu, 2003-11-20 at 16:27, Derrick Guang Yuh Lee wrote:
>
>>dear Ilya
>>
>>thank you for the info, two things though. is there any advantage of
>>having VMD use the xtc file over the tjr file? and you mentioned the -x
>>option of mdrun, i'm not a hundred percent sure what you mean by that,
>>could you please be a bit more detailed about that? thanks.
>>
>>
>> - derrick
>>
>>
>> derrick Lee
>> faculty of Science
>> Memorial University of Newfoundland
>> k24dgyl at mun.ca or derrickglee at hotmail.com
>>
>>"a teacher is never a giver of truth - he is a guide, a pointer to the
>>truth that each student must find for himself. a good teacher is merely a
>>catalyst."
>>                                                              - bruce lee
>>
>>On Thu, 20 Nov 2003, Ilya Chorny wrote:
>>
>>>VMD can read xtc files as well. VMD reads the corrdinates it doesn't
>>>need velocities.
>>>
>>>Set
>>>
>>>nstxtcout = 100
>>>
>>>and don't forget the -x option in mdrun
>>>
>>>Ilya
>>>
>>>
>>>On Thu, 2003-11-20 at 15:40, Derrick Guang Yuh Lee wrote:
>>>
>>>>dear [gmx-users]
>>>>
>>>>i was just curious if someone could help me create a movie for VMD. it had
>>>>just occured to me that i can use my trajectory file (.tjr) to view my
>>>>monolayer in VMD, but because it is 1ns simulation, the file is a little
>>>>too large for VMD and our computers here.
>>>>
>>>>so, would anyone be able to inform me of how i could set it up such that
>>>>my trajectory file prints out the velocities and coordinates of my system
>>>>about 100 times or so? it'd be appreciated. thanks.
>>>>
>>>>
>>>> - derrick
>>>>
>>>> derrick Lee
>>>> faculty of Science
>>>> Memorial University of Newfoundland
>>>> k24dgyl at mun.ca or derrickglee at hotmail.com
>>>>
>>>>"a teacher is never a giver of truth - he is a guide, a pointer to the
>>>>truth that each student must find for himself. a good teacher is merely a
>>>>catalyst."
>>>>                                                              - bruce lee
>>>>
>>>>_______________________________________________
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>>>--
>>>----------------------------------------------------------------
>>>Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
>>>Postdoctoral Researcher   University of California-San Francisco
>>>phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
>>>fax: (415)502-1411        San Francisco, Ca, 94107
>>>            email: ichorny at maxwell.ucsf.edu
>>>----------------------------------------------------------------
>>>
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