VMD-L Mailing List

From: Chris Broomell (ccbroomell_at_gmail.com)
Date: Tue Mar 31 2020 - 15:27:29 CDT

John,

One more thing which may/may not be germaine:

I do get an info msg on startup of a mismatch between CUDA runtime and GPU
driver and that no CUDA accelerator devices are available.
I'm using a NVIDIA RTX 2070 Super...this does have CUDA cores...

I'll try to reinstall the drivers.

Best,
Chris

On Tue, Mar 31, 2020 at 4:21 PM Chris Broomell <ccbroomell_at_gmail.com> wrote:

> Hi John,
>
> Thanks. Here's a basic rundown of the process that I get hung up on.
>
>
> - Working files are 5kep and 1dzl
> - I'll load both molecules
> - select "surface" as the drawing method
> - at this point there's a fairly significant lag (expected)
> - when I try to expand the trajectory to all frames (0:59) this is
> where I start getting the error messages. Indeed VMD usually crashes at
> this point.
> - I have a bit more success using MSMS
> - in this case I CAN get an intact surface representation of the
> large VLP but, sometimes, not all of the frames are displayed.
>
> It is absolutely possible that I am "not doing things properly." I don't
> know what the best practices are for this kind of workflow.
>
> My endgoal will be to generate representations of the intact VLPs with
> various structural elements/sequences highlighted. I'm fine with the
> selections/manipulations, etc., but any time I start trying to employ
> surface features things get wobbly.
>
> Thanks again for your help.
>
> Chris
>
> On Tue, Mar 31, 2020 at 3:49 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi Chris,
>> Which PDB code is running you out of memory? How are you
>> visualizing it? It should be possible to visualize structures
>> with say 5 to 10 million atoms even with only 2GB of memory
>> depending on how it is done. I can give you some advice if you
>> tell me more about what you're doing.
>>
>> Best,
>> John
>>
>> On Mon, Mar 30, 2020 at 04:58:00PM -0400, Chris Broomell 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 <[1]ccbroomell_at_gmail.com> wrote:
>> >
>> > Thanks, John, for the response. Enjoy the bunker!
>> >
>> > Chris
>> >
>> > > On Mar 30, 2020, at 15:01, John Stone <[2]johns_at_ks.uiuc.edu>
>> wrote:
>> > >
>> > > Hi guys,
>> > >Â Catching up on my exploding inbox.
>> > > Thanks Axel and others, everything said so far here is accurate--0000000000003edba105a22c66e4--