VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Mar 02 2018 - 18:15:11 CST

Hi Stuart,

Nope, its still memory. The windows version of VMD is built as a 32-bit application, so that means that once you get of ~4GB allocated, a subsequent memory allocation will fail. Your options are either to stride the trajectory some more, wait until John answers that there is a beta of VMD 64-bit for windows (this is a long standing request. I have no idea what the progress looks like on that front) or my personal favorite, install linux.

-Josh

On 03/02/2018 04:01 PM, Rose, Stuart Wallace 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<mailto:swrose_at_illinois.edu>
University of Illinois @ Urbana-Champaign Office: 153 Davenport Hall
607 S. Mathews Avenue
Urbana, IL 61801
                                                                               Lab Ph. (217)333-7407
Center for Biophysics & Quantitative Biology Office: Loomis, MC-704
*********************************************************************************