VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Mar 02 2018 - 17:53:43 CST

Is that a 32-bit build you have?
It is capped at 4GB memory usage.

Try it on Linux/Mac with a later VMD version and I think it would work.

On Mar 3, 2018 12:26 PM, "Rose, Stuart Wallace" <swrose_at_illinois.edu> wrote:

> vers 1.93 with Cuda support for Windows
>
> ************************************************************
> *********************
> Stuart W. Rose, PhD
> E-Mail: swrose_at_illinois.edu
> University of Illinois @ Urbana-Champaign Office: 153
> Davenport Hall
>
> 607 S. Mathews Avenue
> <https://maps.google.com/?q=607+S.+Mathews+Avenue+%0D%0A+Urbana,+IL+61801&entry=gmail&source=g>
> Urbana, IL 61801
> <https://maps.google.com/?q=607+S.+Mathews+Avenue+%0D%0A+Urbana,+IL+61801&entry=gmail&source=g>
>
>
> Lab Ph. (217)333-7407 <(217)%20333-7407>
> Center for Biophysics & Quantitative Biology Office: Loomis,
> MC-704
> ************************************************************
> *********************
> ------------------------------
> *From:* Ashar Malik [asharjm_at_gmail.com]
> *Sent:* Friday, March 02, 2018 5:25 PM
> *To:* Rose, Stuart Wallace
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: VMD stops furing loading of DCD trajectory
>
> What version of VMD are you using?
>
> On Sat, Mar 3, 2018 at 11:07 AM, Rose, Stuart Wallace <swrose_at_illinois.edu
> > wrote:
>
>> Hello,
>>
>> I know there are work arounds for processing large DCD trajectory files
>> without loading the whole thing into VMD. However I am trying to load a
>> trajectory file and I should have plenty of RAM but VMD keeps quiting. I
>> am running on Windows 10 with 16 GB of ram; 8 processors and one GPU. My
>> trajectory has 942 frames and takes up about 3.5 GB of space. When I start
>> loading DCD trajectory using either animate with "waitfor all" or using the
>> load dialogue with either option of load in background or not, VMD
>> consistently fails at around frame 810.
>>
>> This point of failure occurs if I load separate files with smaller chunks
>> of frames or load frames in batches of 100 right up to around frame 810. I
>> monitor the system memory with task manager and see that the available
>> memory goes from 7.6 GB to about 5.2 GB where VMD stops. I know this is an
>> issue in other posts but there is plenty of memory available in this
>> case. How do I load the trajectory without reducing the number of frames?
>>
>> Regards,
>> Stuart
>>
>> ************************************************************
>> *********************
>> Stuart W. Rose, PhD
>> E-Mail: swrose_at_illinois.edu
>> University of Illinois @ Urbana-Champaign Office: 153
>> Davenport Hall
>>
>> 607 S. Mathews Avenue
>> <https://maps.google.com/?q=607+S.+Mathews+Avenue+%0D%0A+Urbana,+IL+61801&entry=gmail&source=g>
>> Urbana, IL 61801
>> <https://maps.google.com/?q=607+S.+Mathews+Avenue+%0D%0A+Urbana,+IL+61801&entry=gmail&source=g>
>>
>>
>> Lab Ph. (217)333-7407 <(217)%20333-7407>
>> Center for Biophysics & Quantitative Biology Office: Loomis,
>> MC-704
>> ************************************************************
>> *********************
>>
>
>
>
> --
> Best,
> /A
>