İlt: Re: heat annealing conf file

From: Molecular Dynamics (moleculardynamics_at_yahoo.com)
Date: Fri Jun 03 2011 - 09:57:07 CDT

--- 03/06/11 Cum tarihinde Molecular Dynamics <moleculardynamics_at_yahoo.com> şöyle yazıyor:

Kimden: Molecular Dynamics <moleculardynamics_at_yahoo.com>
Konu: Re: namd-l: heat annealing conf file
Kime: "HanShen" <han.shen_at_bme.gatech.edu>
Tarihi: 3 Haziran 2011 Cuma, 17:39

Dear Shen,

Thanks for your reply. I add this commands into my conf file and I got this eror:

TCL: can't read "t": no such variable
FATAL ERROR: can't read "t": no such variable
    while executing
"temperature $t"
    (file "z.namd" line 25)

I want to heat my system form 0 to 300 K without using l langevinPiston and langevinTemp then run the simulation again and keep system 300 K. My conf file is in below. How can I rearrange the conf file to run without any erors ?

Thanks for your help

M

structure              z.psf
coordinates            z.pdb
paratypeCharmm     on
parameters         z.prm

set temperature 0
temperature $t

dielectric      1
cutoff          25.
switching       on
switchdist      22.
pairlistdist    29.

cellBasisVector1  59. 0.0  0.0
cellBasisVector2  0.0 59.  0.0
cellBasisVector3  0.0 0.0  59.

timestep            1
exclude           scaled1-4
1-4scaling  1
nonbondedFreq       5
fullElectFrequency  7
stepspercycle       30

PME             on
PMEGridSizeX    65
PMEGridSizeY    65
PMEGridSizeZ    65

restartfreq         100
dcdfreq             100
xstFreq             100
outputEnergies      1000
outputPressure      100

outputName             zz
restartname            zz_restart
DCDfile                zz.dcd

binaryoutput    no

binaryrestart   yes

set initialTemp    0
set anealTemp      300

set tempDiff [expr $anealTemp-$initialTemp]
set stepNum        250.0
for {set i 0} {$i<=$stepNum} {incr i} {
set t [expr $initialTemp+$tempDiff*($i/$stepNum)]
puts "Info: Setting temperature to $t"

run  100000
}

--- 03/06/11 Cum tarihinde Shen, Han <han.shen_at_bme.gatech.edu> şöyle yazıyor:

Kimden: Shen, Han <han.shen_at_bme.gatech.edu>
Konu: Re: namd-l: heat annealing conf file
Kime: "Molecular Dynamics" <moleculardynamics_at_yahoo.com>
Tarihi: 3 Haziran 2011 Cuma, 16:56

#yiv1585139555 p {margin:0;}Hi,

I have an example here:
******************************************
set initialTemp    300
set anealTemp      550

set tempDiff [expr $anealTemp-$initialTemp]
set stepNum        250.0
for {set i 0} {$i<=$stepNum} {incr i} {
set t [expr $initialTemp+$tempDiff*($i/$stepNum)]
puts "Info: Setting temperature to $t"
langevinTemp          $t
langevinPistonTemp    $t

run  10000
}
******************************************
you can add this at the end of the file and disable the langevinPistonTemp and langevinTemp. Temperature still need to be set at the beginning.

Good luck!

From: "Molecular Dynamics" <moleculardynamics_at_yahoo.com>
To: namd-l_at_ks.uiuc.edu
Sent: Thursday, June 2, 2011 6:26:17 AM
Subject: namd-l: heat annealing conf file

-- 
Han Shen
Wallace H. Coulter Department of Biomedical Engineering
Georgia Institute of Technology and Emory University
Room 4165, M Building
Atlanta, GA 30332
770-676-8397

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