Explicit Water System Condensing

From: Keith Battle (keith.battle_at_gmail.com)
Date: Thu Feb 25 2010 - 09:17:53 CST

Hi NAMD world,

My group has assembled a system for MD consisting of a short peptide
solvated in a TIP3P waterbox atop a fixed crystal surface. The
waterbox contains ~40,000 waters and has a dimension of 94 X 83 X 70
angstroms. We designed the box to give a water density close to 1. We
ran a short 1000 step minimization and MD run at NVE conditions for
10,000 steps just to get a feel for how the system will equilibrate.
After about 5,000 steps into MD we noticed the corners of the waterbox
condensing and forming a vacuum (we used IMD to watch the simulation).
Any insight on how to stop this process would be greatly appreciated.
My input file is given below.

# input
amber yes
coordinates C:/Users/Alan/Desktop/a1_solvated/A_1_system_new.pdb
extendedSystem C:/Users/Alan/Desktop/a1_solvated/test.xsc
parmfile C:/Users/Alan/Desktop/a1_solvated/A_1_system.prmtop

# output
set output C:/Users/Alan/Desktop/a1_solvated/A_1_system_new
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50

binaryoutput no
binaryrestart no
outputEnergies 100
restartfreq 1000

# mobile atom selection:
# protein or waters
fixedAtoms on
fixedAtomsCol O

# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
rigidBonds water

# Simulation space partitioning
switching on
switchdist 9
cutoff 10
pairlistdist 12

# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20
nonbondedFreq 2
fullElectFrequency 4

# Temperature control

set temperature 310
temperature $temperature; # initial temperature

wrapAll on
dcdUnitCell yes

IMDon on ;#
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait yes ;# wait for VMD to connect before running?

# Scripting

minimize 1000
reinitvels $temperature
run 10000


Keith Battle
University of South Alabama

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