Re: How to write gradual heating config file

From: Hyundeok Song (songhk_at_email.uc.edu)
Date: Mon Aug 25 2008 - 19:30:26 CDT

hi Audrey

I did it before by two methods. Both work well.
(changing velocity, reassigning temperature)
1> heated from 0 K
2> heated from 25 K

I attached the code. I remember that reassigning frequency should the multiple of stepspercycle.

hyun.

**********************************************************

1> heating by changing velocity.

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# Ubiquitin in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ubq_wb.psf
coordinates ubq_wb.pdb

set temperature 310
set outputname ubq_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 42. 0. 0.
cellBasisVector2 0. 44. 0.
cellBasisVector3 0. 0 47.
cellOrigin 31. 29. 17.5

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 100

set freq 10

for {set i 0} {$i <= $temperature} {incr i} {
langevinTemp $i
reinitvels $i
run $freq
}

run 5000

2> heating by reassigning temperature.

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# Ubiquitin in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ubq_wb.psf
coordinates ubq_wb.pdb

set temperature 310
set outputname ubq_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 42. 0. 0.
cellBasisVector2 0. 44. 0.
cellBasisVector3 0. 0 47.
cellOrigin 31. 29. 17.5

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# For heating, use temperature reassignment.
reassignFreq 5
reassignTemp 0
reassignIncr 1
reassignHold 310

# Minimization
minimize 100

run 5000

---- Original message ----
>Date: Mon, 25 Aug 2008 17:41:59 -0500
>From: "Audrey Salazar" <alsalazar_at_u.northwestern.edu>
>Subject: namd-l: How to write gradual heating config file
>To: namd-l_at_ks.uiuc.edu
>
>Dear NAMD-L,
>I am fairly new to NAMD and thus far, I have been able to navigate
>through NAMD and VMD using information from the tutorials. I would
>like to know if it is possible to make a script in the .conf file to
>perform gradual heating.
>
>After searching the NAMD-L archive for "gradual heating" I came upon
>this thread:
>http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6440.html
>where Victor Ovchinnikov says that he includes a snippet of his code,
>but the snippet is not available on the archive.
>
>I realize from reading the Config file tutorial page
>(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html)
>that after commands like "run" or "minimize" that only a subset of
>commands may be used, but I am not sure what kind of a resource I
>should look for to do this.
>
>Example scripts would be especially helpful.
>
>Thank you in advance.
>
>Audrey
>
>
>
>--
>Audrey L. Salazar
>Amaral Research Group
>Dept. of Chemical and Biological Engineering
>Northwestern University
>Evanston, IL USA
>Phone: 847.491.2188
>


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