From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Jun 23 2016 - 08:45:54 CDT
You have a problem with your brackets and braces:
set groupId2 { [ 11 12 13 14 15 16 17 18 19 20 } ]
ββββββββββββββββββββββββββββββββββββββββββ
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us
On Thu, Jun 23, 2016 at 8:01 AM, Sarah Sweger <swegers_at_duq.edu> wrote:
> Dear NAMD Users:
>
>
> I have written a simple tcl code to implement into NAMD through NAMD
> tclForces to track the length of time a simulation runs based off of
> distance between two proteins. The code below takes atom coordinates from
> two proteins and sets them to groupId1 and groupId2 ( I have replaced the
> numbers for simplicity, the actual system has over 6000 atoms). The
> calcforces loads the coordinates from each group and calculates a distance
> between each group. I want to stop the simulation based off of certain
> distance parameters. The exit command should exit cleanly and write the
> output files when one of the parameters of the if statement is met. However,
> it stops running the NAMD simulation but does not actually exit or write the
> output files. I cannot figure out why this is occurring or any other way to
> achieve the goal.
>
>
> Thanks,
>
> Sarah
>
>
> set groupId1 { [ 1 2 3 4 5 6 7 8 9 10 ] }
>
> set groupId2 { [ 11 12 13 14 15 16 17 18 19 20 } ]
>
> proc calcforces { } {
> global groupId1 groupId2
>
> loadcoords p
>
> set dist [ getbond $p($groupId1) $p($groupId2) ]
> print $dist
>
> if { $dist <= 42.5 || $dist >= 50 } {
> print "exiting"
> print $dist
> exit
> }
> }
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:34 CST