VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Mar 07 2019 - 20:58:58 CST

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> 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>
> *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 <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>
> *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*
>
>
>