From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Oct 20 2015 - 01:23:57 CDT
Did you actually used a veldcd ?
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Jhonatam Cordeiro Rodrigues
Gesendet: Montag, 19. Oktober 2015 22:08
An: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Betreff: namd-l: How to calculate the temperature for a subset of my simulation
Dear NAMD users
I am running simulations that have different temperature couplings on different subsets of the simulation. Please, how can I read the temperature for a given selection of atoms?
I found this nice script written by Shailesh Pandey, but when I run it, I get temperature readings that are certainly incorrect (over 1Bi K).
Is there something wrong with the script? or is there a script out there that would do the trick?
########### TCL script to calculate temperature from velocity trajectorySTART #########
# rigidbonds none=0; water=1; all=2
proc getTemp { frame rigidbonds } {
set all [atomselect top all frame $frame]
set eng {};
set esum 0.0;
set nDoF 0;
set c1 [[ atomselect top "((type 'HW' or hydrogen) or water)" ] get index ]
set c2 [[ atomselect top "water" ] get index ]
foreach m [$all get mass] v [$all get {x y z}] id [$all get index] {
set e [expr {0.5 * $m * [vecdot $v $v]}]
# lappend eng $e
set esum [expr {$esum + $e}]
# set all [atomselect top all frame $frame]
set DoF 3
#SHAKE?
if { ($rigidbonds == 2) && ($id in $c1) } {
set DoF 2
} elseif { ($rigidbonds == 1) && ($id in $c2) } {
set DoF 2
}
set nDoF [expr {$nDoF + $DoF}]
}
$all delete
puts "nDoF: $nDoF, esum: $esum"
set kB 0.00198657 ;# kcal/(mol.K)
set T [expr { $esum * 2.0 / ($nDoF * $kB) }]
puts "Frame: $frame ## Temp: $T"
}
########### TCL script to calculate temperature from velocity trajectory END #########
After the running the script for water I get results like this:
nDoF: 481968, esum: 638805356005.8174
Frame: 201 ## Temp: 1334370608.0432146
Sincerely
Jhonatam Cordeiro,
Ph.D. candidate
Department of Industrial & Systems Engineering
North Carolina A&T State University
1601, East Market st.
Greensboro, NC 27411
Phone: +1 336 706-9203
Fax: +1 336 334-7729
email: jcrodrig_at_aggies.nc <http://goog_74760233> at.edu <http://at.edu>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:25 CST