VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 06 2015 - 09:53:56 CST

Hi,
  In the molecule file browser (File | New Molecule, or File | Load Data Into..)
below the filename/browse button and the file type selector in the lower
left corner, you will see "Frames" and controls for first/last/stride, those
are how you can control what frames VMD loads from a file. When using the
graphical interface. There are also analogous parameters to the "mol new"
and "mol addfile" text commands.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 06, 2015 at 03:32:57PM +0000, Eiros Zamora, Juan wrote:
> Dear John,
>
> Thanks for the reply. Is there a way to specify the stride of frames when loading the MD trajectory through the command line? Been looking around on how to change this without success.
>
> Best,
>
> Juan
>
>
> > On 2 Nov 2015, at 16:35, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > The current VMD builds for MacOS X are 32-bit (long story with
> > cross-platform GUI toolkits not working well enough with the new Cocoa APIs).
> > As such, the data size that you can load and work with is limited by 32-bit
> > addressing even though you're running on a 64-bit machine with large physical
> > memory. You will need to limit the size of the data you load to fit within
> > the addressing limit, under 4GB. You can do this by having VMD load a subset
> > of trajectory frames at a time, either by changing the first/last frames
> > loaded, or by changing the stride it uses when loading the frames.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Nov 02, 2015 at 09:35:36AM +0000, Eiros Zamora, Juan wrote:
> >> Dear VMD users,
> >>
> >> I recently installed VMD 1.9.2
> >> ??? MacOS X OpenGL (32-bit Intel x86) (Apple MacOS-X (10.4.7 or later) with hardware OpenGL (native bundle))
> >> on a new iMac with the following specs:
> >>
> >> OS X El Capitan
> >> Version 10.11.1
> >> Processor 4 GHz Intel Core i7
> >> Memory 8 GB 1867 MHz DDR3
> >> Graphics AMD Radeon R9 M395 2048 MB
> >>
> >> I tried loading a netcdf trajectory that I obtained with AMBER split in chunks, in total its around 6GB of data.
> >>
> >> I got the following error
> >>
> >>> VMD(63006,0xa344c000) malloc: *** mach_vm_map(size=8388608) failed (error code=3)
> >>> *** error: can't allocate region
> >>> *** set a breakpoint in malloc_error_break to debug
> >>> putget.c:3593: failed assertion `value != NULL'
> >>> Abort trap: 6
> >>
> >> I tried to attach a more complete error message on a 54 KB text file, but the message didn???t reach the mailing list, so I can email it off-list if need be.
> >>
> >> I googled the error and saw some similar problems on this mailing list, but they were from 2007 to 2011.
> >> I understand that this is related to the 32-bit version of VMD for Mac, is there any solution to this now (as in, can I get a 64-bit version)? Also, would installing the CUDA version make any difference? I presume not, but just to be sure that I am installing the most appropriate version of VMD for this machine???
> >>
> >> Thanks for any suggestions,
> >>
> >> Juan Eiros
> >
> > --
> > 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/
> 

-- 
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/