VMD-L Mailing List
From: Maximilian Ebert (m.ebert_at_umontreal.ca)
Date: Wed Feb 27 2013 - 15:59:32 CST
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Hi,
Thanks again. For now I will just use my code but indeed not to manage the trajectory loading would make many things easier. The feature will be super useful to many researchers I guess and make the whole analysis easier for less skilled users.
Greets,
Max
Dipl.-Ing. Maximilian Ebert
Étudiant au doctorat en biochimie
Laboratoire du Dr. Joelle Pelletier
Université de Montréal
On 2013-02-27, at 11:34 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> I think that the BigDCD script is currently the easiest way to do
> the sort of analysis that you're describing, since you don't have to
> explicitly manage the trajectory loading process. I'm working on extending
> VMD to allow arbitrary out-of-core access to huge trajectory files without
> having to do things in either of the ways we've just discussed, but that
> feature is still a ways off yet.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 26, 2013 at 05:35:54PM -0500, Maximilian Ebert wrote:
>> Hi John,
>>
>> Thank you for your prompt answer. I am using mol load and mol delete to empty my RAM. The trajectory file is too large to load it completely. So I split it into smaller pieces to calculate the bfactor for the complete simulation. I load a 2GB DCD pull out the information of all frames, store them in an array, go to next fragment trajectory, do the same and finally calculate the bfactor.
>>
>> If there is a better way to handle large files in VMD I am always happy to know about it. (I saw Read Big DCD Files but I thought this way the calculations would be faster)
>>
>> Anyhow I will change my code from mol load to mol new just in case you will remove the load command. Maybe you should mention in http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html that load is deprecated.
>>
>> Thank you very much,
>>
>> Dipl.-Ing. Maximilian Ebert
>>
>> Étudiant au doctorat en biochimie
>> Laboratoire du Dr. Joelle Pelletier
>> Université de Montréal
>>
>> m.ebert_at_umontreal.ca
>>
>> On 2013-02-26, at 5:16 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>>>
>>> Max,
>>> At present there's not a way to silence the console output, but I wouldn't
>>> have expected you to get massive console output from just loading 20 files.
>>> Are you loading each of the trajectories into a separate molecule for
>>> a particular reason? You should be using the newer "mol new" and "mol addfile"
>>> syntax when loading files, as the old "mol load" syntax is now deprecated
>>> and will be removed from the program eventually.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Tue, Feb 26, 2013 at 04:52:38PM -0500, Maximilian Ebert wrote:
>>>> Hi list,
>>>>
>>>> I wrote a Tcl script to calculate the bfactor from a trajectory which was split into many pieces because the trajectory itself is too large to load as one file. It is working but now I want to execute it with less output. Since I load more than 20 trajectories I don't want to see the output of:
>>>>
>>>> mol load psf $psffile dcd $item
>>>>
>>>> Is there a possibility to suppress it in the console? In addition, I wanted to know if someone knows why the Tcl console GUI is so slow compared to the console window? I am using Mac OS X 10.8.2 and vmd 1.9.1.
>>>>
>>>> Thank you very much,
>>>>
>>>> Max
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
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