From: Jhonatam Cordeiro Rodrigues (jcrodrig_at_aggies.ncat.edu)
Date: Tue Oct 20 2015 - 13:47:53 CDT
Dear NAMD users
After using the right files (.veldcd). The script generated values that are
also incorrect. After running the script I got values like this:
nDoF: 481968, esum: 638805356005.8174
Frame: 201 ## Temp: 4.08764523
Please, what am I missing?
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
On Tue, Oct 20, 2015 at 1:20 PM, Jhonatam Cordeiro Rodrigues <
jcrodrig_at_aggies.ncat.edu> wrote:
> 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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