VMD-L Mailing List

From: Oliver Beckstein (orbeckst_at_jhmi.edu)
Date: Wed Nov 21 2007 - 19:13:32 CST

Thomas,

thank you for the offer but what I'm actually doing is a selection like

    water and not within 3.5 of (protein and not hydrogen)

and then calculating the density of the (dynamic) selection with the
VolMap plugin.

> are you interested in reducing the size of your trajectories by
> deleting every
> atom that is longer than a cuttof distance (you can define this) from
> your
> macromolecule/s. In this way you can make them more "handy". I have
> written a
> tcl script that does this job automatically, if you're interested let
> me know
> and I'll send it to you.

At the moment I am using MDAnalysis tools (python/numpy), which works
really nicely but VMD's dynamic distance selections are actually very
fast and so I wouldn't mind taking advantage of it.

Best wishes,
Oliver

> regards,
> Thomas
>
>>
>> Oliver,
>> Please see the "BigDCD" plugin in the VMD script library, or that
>> has been posted to the VMD-L last a few times in the last few weeks.
>> Let us know if you have questions.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Tue, Nov 20, 2007 at 03:28:45PM -0500, Oliver Beckstein wrote:
>>> Hi,
>>>
>>> is there a way to analyse trajectories that are bigger than the
>>> available RAM? For instance, I have trajectories > 5GiB in size that
>>> I
>>> would like to analyze with VolMap but they can't be loaded because
>>> VMD
>>> insists on keeping the whole trajectory in memory.
>>>
>>> A cumbersome work-around would be to split the trajectory into
>>> smaller
>>> chunks, run volmap on each chunk, then average the resulting dx
>>> files.
>>> However, I can think of situations when a simple average is not
>>> enough
>>> (for instance for time correlation functions) and it would very
>>> convenient if one could just have a (python-style) iterator over a
>>> trajectory (similar to the 'for timestep in universe.dcd: ....' idiom
>>> in http://code.google.com/p/mdanalysis/ ).
>>>
>>> (Note: I don't think that increasing swap space is a solution because
>>> that leads to the computer almost grinding to halt when the
>>> trajectory
>>> is loaded.)
>>>
>>> Thanks,
>>> Oliver
>>>
>>> --
>>> Oliver Beckstein * orbeckst_at_jhmi.edu
>>>
>>> Johns Hopkins University, School of Medicine
>>> Dept. of Physiology, Biophysics 206
>>> 725 N. Wolfe St
>>> Baltimore, MD 21205, USA
>>>
>>> Tel.: +1 (410) 614-4435
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>
>
> 

--
Oliver Beckstein * orbeckst_at_jhmi.edu
Johns Hopkins University, School of Medicine
Dept. of Physiology, Biophysics 206
725 N. Wolfe St
Baltimore, MD 21205, USA
Tel.: +1 (410) 614-4435