Finding size of water box

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Mon Aug 06 2007 - 11:15:41 CDT

Dear NAMD-L
I am a first year graduate student studying nucleic acids using the
all27 force field in NAMD. At present, I am interested in making a
short, single stranded RNA solvated with water molecules that I can
run as a test in NAMD. Below, I outline my procedure intermingled
with questions, highlighted by the **. I would appreciate any help
that the NAMD community might be able to provide.

At present, I am building a config file and I am under the impression
that I need to give the size of the water box surrounding my RNA so
that I can have periodic boundary conditions.

** To have periodic boundary conditions, must I specify the size of
the water box surrounding my molecule? If so, how do I determine the
size of the water box using my automatically generated psf and/or pdb
file? I will include my config file below.

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

# Minimization and Equilibration of
# Nucleic Acid (GCA) in a Water Box

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

structure sRNA_autopsf.psf
coordinates sRNA_autopsf.pdb

set temperature 310
set outputname sRNA_GCA

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_na.prm
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching on
switchdist 10.
pairlistdist 14

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2# 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 no ;# don't couple langevin bath to hydrogens

# Output
outputName $outputname

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

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

## I have seen the dimensions of the repeating unit for periodic
boundary conditions here##

Thank you in advance.

Audrey Salazar

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

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