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.
set output C:/Users/Alan/Desktop/a1_solvated/A_1_system_new
# mobile atom selection:
# protein or waters
# Basic dynamics
# Simulation space partitioning
# Multiple timestepping
# Temperature control
set temperature 310
temperature $temperature; # initial temperature
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?
University of South Alabama
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