VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Mar 07 2019 - 21:13:36 CST

Hey Peter, I will give that a try. I also notice another potential memory issue with volmap. I can't get volmap to work beyond 30,000 frames without VMD crashing. I wonder if the BigDCD plugin would fix this memory issue as well...?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Peter Freddolino <petefred_at_umich.edu>
Sent: Thursday, March 7, 2019 7:58 PM
To: McGuire, Kelly
Cc: Bennion, Brian; VMD Mailing LIst
Subject: Re: vmd-l: Re: VMD Text Mode

Short answer is yes, you're still going to be memory limited. Possible solutions are loading only one every n frames, doing some analysis on trajectories with water removed, or using bigdcd (https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/).
BTW, you may want to get into the habit of adding 'waitfor all' to the end of your load commands if you're working with big trajectories. Otherwise the tcl interpreter can move on after the load starts but before it finishes, which can also lead to odd looking results downstream.
Best,
Peter

On Thu, Mar 7, 2019 at 9:53 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
I tried this on Linux, RHEL7 and Ubuntu. RHEL7 is on the supercomputer and has 123 GB RAM available on the system I use for VMD. I was able to open 38,000 frames on RHEL7, but couldn't get the full 90,000. My DCD is 75 GB in size.

Ubuntu was local, so it had 32 GB RAM available. I was only able to get 3,200 frames loaded in text mode.

VMD does not crash, it just loads a reduced number of frames.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>>
Sent: Thursday, March 7, 2019 6:07 PM
To: McGuire, Kelly; VMD Mailing LIst
Subject: RE: VMD Text Mode

Does the vmd session crash? What is your hardware/OS that you are using for the textmode session?

Brian

From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> On Behalf Of McGuire, Kelly
Sent: Thursday, March 7, 2019 4:02 PM
To: VMD Mailing LIst <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: vmd-l: VMD Text Mode

I am trying VMD text mode for the first time since I have really large DCD files. I tried loading my DCD, but it doesn't seem to load all of the frames. I do:

mol new Simulation_QwikMD.psf type psf

mol addfile MD1.dcd type dcd first 0 last -1 step 1

There should be 90,000 frames, but i only loads ~3,200 frames. What am I doing wrong? Is VMD text mode still RAM dependent for DCD file sizes that can be loaded?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602