From: Jhonatam Cordeiro Rodrigues (jcrodrig_at_aggies.ncat.edu)
Date: Tue Oct 20 2015 - 12:20:46 CDT
Hello Norman
Thank you for the suggestion. I was using the wrong file. I was loading the
.dcd instead of the .veldcd.
Thankfully
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
On Tue, Oct 20, 2015 at 2:23 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> 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
>
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