VMD-L Mailing List

From: Smolin, Nikolai (nikolai.smolin_at_gmail.com)
Date: Fri Jan 06 2017 - 09:15:49 CST

Thanks!
I guess it is same problem with Macs?

---------------------------------------------------------------------------------------------------------
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
E-mail : nikolai.smolin_at_gmail.com
E-mail : nsmolin_at_luc.edu
in: https://www.linkedin.com/in/nikolaismolin
www : https://sites.google.com/site/nikolaismolin/

On Fri, Jan 6, 2017 at 2:14 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:

> 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
>> E-mail : <mailto:nikolai.smolin_at_gmail.com> nikolai.smolin_at_gmail.com<mailt
>> o:nikolai.smolin_at_gmail.com>
>> E-mail : <mailto:nsmolin_at_luc.edu> nsmolin_at_luc.edu<mailto:nsmolin_at_luc.edu>
>> in: <https://www.linkedin.com/in/nikolaismolin>
>> https://www.linkedin.com/in/nikolaismolin
>> www : <https://sites.google.com/site/nikolaismolin/>
>> https://sites.google.com/site/nikolaismolin/
>>
>>
>>
>