Re: NAMD log file analysis script problem (namdstats.tcl)

From: Demet Akten (demet.akten_at_gmail.com)
Date: Sun Jun 15 2008 - 03:35:49 CDT

Hi,

In "proc data_time", the second while loop should be changed to;
while { [gets $file line] != -1 } {
   if [regexp "ENERGY: " $line] {set ener "$ener $line"}
   if {[regexp "ENERGY: 1" $line]} {set ener "$ener $line"}
}

this will make sure that it will skip to 1000000 steps. Similaryly,
if you want to exceed 1999999 and read 2000000, you should change it to;
while { [gets $file line] != -1 } {
   if [regexp "ENERGY: " $line] {set ener "$ener $line"}
   if {[regexp "ENERGY: 1" $line] || [regexp "ENERGY: 2" $line]} {set
ener "$ener $line"}
}

and so on ....

Demet

On Jun 14, 2008, at 9:39 PM, sudipta sinha wrote:
> Hi All,
> I am facing a problem regarding namdstats.tcl script. I
> want to
> analyze average properties and instantaneous properties of
> NAMD .log
> file. I have run the script through VMD Tkconsole. The script
> calculates only up to 1000000 steps. But my simulation have 1700000
> steps. I
> am getting a error in VMD Tkconsole like this
>
> *ERROR:*can't read "e(101,2)": no such element in array
>
> How I over come this problem by modifying the namdstats.tcl
> script. I am
> also attaching this file. If anybody suggest me where do I change this
> script?
>
> Thanks and regards
> sudipta

Demet Akten-Akdogan, Ph.D.
Research Associate
Polymer Research Center
Bogazici University
email: demet.akten_at_gmail.com

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