VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jan 06 2017 - 02:14:07 CST

Hi Nikolai!

Requests for a 64 bit build have appeared previously
<http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17267.html>:) But
until then you can load less frames, or remove the solvent or preform your
analysis in chunks (Load 2GB, do the analysis, delete the frames, load next
2GB etc...).
There is also a 64 bit build of CatDCD
<http://rpm.lammps.org/windows/testing/>that you can use to split your
trajectory and or remove solvent...
Finally, for what it's worth Chimera
<https://www.cgl.ucsf.edu/chimera/download.html>does have a 64 bit windows
build. For trajectory analysis it's a bit slower than VMD, but still fine.

Best,
Ajasja

On 6 January 2017 at 00:14, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:

> Hi Nikolai,
>
> I'm pretty sure you are running into the limitations of the 32-bit windows
> build. 32-bit addressable memory space is 4GB, which you will exceed
> greatly with what you are describing here. Linux will work since those
> builds are usually 64-bit, and then you are limited more or less entirely
> by the physical RAM on the machine. The error message could be more helpful
> in this case, but that is what is going on.
>
> -Josh
>
> On 01/05/2017 03:59 PM, Smolin, Nikolai wrote:
> Sear VMD users,
>
> I am trying to load big xtc file in VMD 1.9.3 (also tried 1.9.1 and 1.9.2)
> in Windows 7.
>
> Files size : about 24 GB, 100k frames about 70k atoms.
>
> after loading about 10% of trajectory I am recievieng following error
> message:
>
> gromacsplugin) Error reading timestep, file does not match format.
>
>
>
> I am able to load whole file in Linux using VMD1.9.1
>
> Any suggestions?
>
>
> Thanks
>
> Nikolai
>
>
>
> ------------------------------------------------------------
> ---------------------------------------------
> Nikolai Smolin, Ph.D.
> Staff Scientist
> Department of Cell and Molecular Physiology
> Center for Translational Research and Education
> Loyola University Chicago
> 2160 South First Avenue
> Maywood, IL 60153
> Phone : (708) 216-5158
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>
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