VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Fri Apr 22 2005 - 10:44:25 CDT

Hi John,

Sorry ... I had never paid any attention to the lower left corner of
the New Molecule File Browser until seeing your message. That is great!
I hope from now on a larger number of people may pay more attention to
and use this feature to ease their daily operations on loading
trajectories.

Marc
On Apr 22, 2005, at 11:21 AM, John Stone wrote:

> Marc,
> VMD _DOES_ implement 4) already!!! (quite some time ago)
> You need to set the fields in the "Frames" area of the molecule
> file browser window. By setting "first", "last", and "stride"
> you can load only a subset of the frames in your DCD file.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Apr 22, 2005 at 10:15:17AM -0400, Marc Q. Ma wrote:
>> Kos,
>>
>> Some sugestions:
>>
>> 1. Use a computer system with larger memory. 1, 2, 4GB. The larger,
>> the
>> faster.
>>
>> 2. When you produce the trajectories, save less frequently, say every
>> 1ps per frame. Do not do it every 10fs per frame.
>>
>> 3. Or you may save as often as you wish (for whatever purposes), but
>> you need a DCD_SPLITTER program to split the DCD files -- say save
>> 1/10 of total number of frames to new files, and load these new files
>> for analysis.
>>
>> 4. This maybe a nice feature, however, VMD still does not have: when a
>> user load a dcd file, let the user control how many frames to load,
>> how
>> many frames to skip -- similar to what is provided for "Delete Frames"
>> after all frames are loaded. This way, researchers can quickly check
>> the trajectories without loading all frames.
>>
>> All above is related to allowing VMD to have ample computer memory to
>> show graphics.
>>
>> John: Do you think (4) is a good feature to be added to VMD? I think
>> it
>> will be cool. Currently, my group is using Suggestion #2. This is not
>> the best solution since the more we save, the more we can infer from
>> our simulations.
>>
>> Marc
>> On Apr 21, 2005, at 9:29 PM, Kos wrote:
>>
>>>
>>>
>>> Hi,
>>>
>>> We analyze large trajectory files with SALT IONS, WATERS, APROTININ
>>> (30000 atoms) produced by NAMD. We run them in a linux cluster and we
>>> analyze them in dual Intel Xeon system with VMD (Windows XP) using
>>> Exceed- (X-Windows). As long as the .dcd files are small around 300MB
>>> we didn't encounter problems analyzing them with X-VMD(Exceed) or
>>> even
>>> ftp the .dcd files in the Windows PC from Linux OS and analyze them
>>> directly with VMD for Windows.
>>>
>>> The problem is that when we analyze large 1ns .dcd file the X-VMD
>>> dissapears/crashes and can't read. When we transfer the files to
>>> Windows PC and try VMD there error for the trajectory file:'can't
>>> load
>>> , can't read the time etc'. Are there limitations in VMD? I noticed
>>> that for 10000frames is very slow to load and crashes.
>>>
>>> Is CHARMM an alternative solution to these problems and can treat
>>> large files faster because doesn't need graphics? A general question:
>>> Is CHARMM a more advanced package for MD analysis although not so
>>> friendly and how does compare in the postprocessing part with VMD?
>>>
>>> kos
>>>
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>
> --
> 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
>