VMD-L Mailing List

From: Monika Kumari (Monika.Kumari_at_chemistry.iitd.ac.in)
Date: Wed Jul 31 2019 - 00:22:34 CDT

Dear Users,
I am trying to wrap my trajectory using VMD but due to the larger size, I
am unable to do it without breaking it in smaller sized trajectories. I am
trying to use bigdcd for the same but the script is not working well and
gets aborted at frame 1. Following is the tcl script which I am using.
Please let me know the possible errors I am having in it.

source bigdcd.tcl
package require pbctools
proc wp { frame } {
global sel nf
$sel [pbc unwrap -first 0]
$sel [pbc wrap -centersel "protein" -center com -compound residue -all]
$sel [animate write dcd Wrapped.dcd]
}
mol load psf ../../../make-system/new/ionized.psf
set sel [atomselect top all]
set nf [molinfo top get numframes]
bigdcd wp ../step1-fixed.dcd
bigdcd_wait
quit

And the error I got is copied here:

Info) Using plugin dcd for coordinates from file ../step1-fixed.dcd
after#0
bigdcd aborting at frame 1

Thank you
Monika