VMD-L Mailing List

From: Eiros Zamora, Juan (j.eiros-zamora14_at_imperial.ac.uk)
Date: Tue Feb 02 2016 - 04:15:57 CST

Thanks for the help! That works just fine. Just a quick Q, this does not seem to accept wildcard notation, does it?

For example, say I’ve got a variable number of trajectories,
could I do something like:

mol addfile traj*.nc start 0 step 30 waitfor all

so I don’t have to do a new file in the script for every trajectory file.

Cheers
Juan

On 28 Jan 2016, at 20:19, Ashar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>> wrote:

I use scripts. You should make 1 instead of from command line
I work with DCD type trajectory files so what I do is

#load structure file
mol new structure.psf

#load 1st DCD trajectory file
mol addfile traj0.dcd waitfor all
#load 2nd DCD trajectory file as a continuation of first
mol addfile traj9.dcd waitfor all

you can include first, last and step in the trajectory loading command. So your command should look like:
mol addfile traj.dcd first 0 step 30 waitfor all

using first 0 will start loading from the start -- and load till the end of the trajectory. Step value of 30 will load every 30th Frame. Change the number 30 to however many frames you want to jump.

I use this with DCD style trajectory files, but in theory this should work with all types of files. You can load as many trajectories as you want as long as your system's hardware supports it.

Hope this helps.

Best,
/A


On Fri, Jan 29, 2016 at 5:07 AM, Eiros Zamora, Juan <j.eiros-zamora14_at_imperial.ac.uk<mailto:j.eiros-zamora14_at_imperial.ac.uk>> wrote:
Dear VMD experts,

I like to load trajectories from the command line like so:
$ vmd top.prmtop traj*.nc

Unfortunately, some are too long and VMD crashes. Is there a way to specify from the command line the stride to be used when loading them?

Cheers
Juan




--
Best,
/A