VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jun 10 2017 - 02:15:30 CDT

Hi Sidra,

VMD 32bit has a 4GB cap.
To by pass this issue you can do the following:

1) Load limited frames instead of the entire trajectory.
2) Load a part of your system instead of your entire system. E.g. if you
system is solvated protein - you can load only the protein and not the
solvent. This will reduce used memory.

for 1) I am guessing you use the graphical interface - in which case load
the structure file and load your trajectory. Prior to pressing load there
will be three boxes in the new molecule browse window - first || last ||
stride --- use 0 in first -1 in last and maybe 100 in stride. This will
load every 100th frame.

for 2) you have to make use of the catdcd plugin to strip your trajectory
into a trajectory holding just your system of interest and then load that
into VMD.

Hope this is helpful - if you are still struggling write back.

Best,
/A

On Sat, Jun 10, 2017 at 5:34 PM, Sidra Rafi <sidrarafi89_at_gmail.com> wrote:

> Hi,
>
> I am facing VMD crashed problem while opening my trajectories file. it
> contain 1660 frames.
> I have 8GB RAM and 8X 2.8 GHz processor in my system. I have 2 queries
> related to it.
>
> 1. Is that enough system configuration for vmd?
> 2. Is there anyway to allocate full memory to VMD?
>
> Please help me in this regard,
>
> Sidra
>
>
>
>
> 

-- 
Best,
/A