VMD-L Mailing List

From: ccbroomell_at_gmail.com
Date: Mon Mar 30 2020 - 18:26:00 CDT

Giacomo,

Thanks for the input. I will look for tutorials on how to reduce the number of atoms. If you (or anyone) is willing to point me in a good direction I’d appreciate it.

I’m fairly new to VMD and haven’t really done much of anything from the command line. Not opposed to plugging away at it, though.

Chris

> On Mar 30, 2020, at 17:51, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> 
> Hi Chris, that may work. But most likely graphics wouldn't work properly, and your best bet would be using the text-mode Linux build.
>
> Obviously a text-only build is completely useless for visualization. But it would still be functional for alternative tasks, such as reducing the number of atoms in the structure by saving it into a smaller file that you visualize later with the 32-bit native Windows build.
>
> That would require using the Tcl command line. But that would be a good thing to do with huge structures regardless, so that you can automate analysis tasks that would take too long for an interactive session.
>
> Giacomo
>
>
>
>
>> On Mon, Mar 30, 2020 at 5:38 PM Chris Broomell <ccbroomell_at_gmail.com> wrote:
>> All,
>>
>> One more question:
>>
>> Would it be a feasible workaround if I created a subsystem for Linux on my Windows machine and ran the 64-bit build for Linux that way (I do have 64-bit Win10)? Forgive me if this is an ignorant question...I'm ignorant.
>>
>> Absent something like this is sounds like I'm sunk until there's a 64-bit Windows build available. That being the case...any recommendations for working with large pdb files (i'm only doing structural visualizations...no dynamics).
>>
>> Thanks for your forbearance.
>>
>> Chris
>>
>>> On Mon, Mar 30, 2020 at 3:49 PM <ccbroomell_at_gmail.com> wrote:
>>> Thanks, John, for the response. Enjoy the bunker!
>>>
>>> Chris
>>>
>>> > On Mar 30, 2020, at 15:01, John Stone <johns_at_ks.uiuc.edu> wrote:
>>> >
>>> > Hi guys,
>>> > Catching up on my exploding inbox.
>>> > Thanks Axel and others, everything said so far here is accurate.
>>> >
>>> > I myself have been holding my breath too long for some of the issues
>>> > on 64-bit APIs to be resolved.
>>> >
>>> > The path forward is that I'll make 64-bit VMD builds available, and the
>>> > features that have 64-bit support will be included, and those that
>>> > don't simply will not.
>>> >
>>> > I'm looking at workarounds for issues like the proprietary 3-D input
>>> > device APIs. Some features like the hardware accelerated interactive
>>> > ray tracing engines on Intel and NVIDIA's hardware only support 64-bit
>>> > Windows anyway. We'll likely lose a few features, but we'll gain others,
>>> > and the users can choose the best version for the job.
>>> >
>>> > I've got a Windows system in my home office / bunker / homeschool classroom
>>> > here during lockdown, so I should be able to work on this despite the
>>> > current situation with IL state lockdown etc.
>>> >
>>> > Best,
>>> > John
>>> >
>>> >> On Mon, Mar 30, 2020 at 02:21:25PM -0400, Mortimer Hemmit wrote:
>>> >> Here's one example:
>>> >> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21572.html
>>> >>
>>> >>> On Mon, Mar 30, 2020 at 2:11 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>> >>>
>>> >>> yes, but don't hold your breath.
>>> >>> if you search the mailing list archive, you will find multiple discussion on the subject and explanations for why there is no 64-bit windows version yet.
>>> >>>
>>> >>> Axel.
>>> >>>
>>> >>> On Mon, Mar 30, 2020 at 1:31 PM <ccbroomell_at_gmail.com> wrote:
>>> >>>>
>>> >>>> Thanks for the response. Is there any plan to develop a 64 bit windows build?
>>> >>>>
>>> >>>> Chris
>>> >>>>
>>> >>>> On Mar 30, 2020, at 13:12, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>> >>>>
>>> >>>> ???
>>> >>>> The VMD windows binary is 32bit and thus memory is limited. To use more RAM you would need to run on a different OS for which a 64bit binary is available.
>>> >>>>
>>> >>>> --
>>> >>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> >>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> >>>> International Centre for Theoretical Physics, Trieste, Italy
>>> >>>>
>>> >>>> On Mon, Mar 30, 2020, 12:39 Chris Broomell <ccbroomell_at_gmail.com> wrote:
>>> >>>>>
>>> >>>>> Hi,
>>> >>>>>
>>> >>>>> I am comparing structures of larger VLPs and have been running into issues when analyzing large files. Typical errors include "failed to increase display list memory pool size, system out of memory." I'm working with surface maps (both the shipped flavor as well as MSMS)...mostly cryo and Xray structures of larger VLPs.
>>> >>>>>
>>> >>>>> Is it possible to change the amount of memory that is allocated for VMD processes?
>>> >>>>>
>>> >>>>> If not - are there any recommendations for how to optimize my system to mitigate this?
>>> >>>>>
>>> >>>>> My system is:
>>> >>>>> Win10
>>> >>>>> 16GB RAM
>>> >>>>> NVIDIA RTX 2070 super (6GB DDR6)
>>> >>>>>
>>> >>>>> Thanks in advance for any help that you could offer.
>>> >>>>>
>>> >>>>> Chris
>>> >>>
>>> >>>
>>> >>>
>>> >>> --
>>> >>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> >>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> >>> International Centre for Theoretical Physics, Trieste. Italy.
>>> >
>>> > --
>>> > 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/
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin