Reassure fluctuations in course of simulation

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Jan 20 2014 - 03:19:51 CST

Dear Namd users!

During analysis of the MD trajectory of the water soluble proteins I've
noticed very big pressure fluctuations in course of simulation (Between
-100 to +100 Bar). Below you can see the parameters of the NPT modelling
for simulation of my water soluble protein

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp 310

How can I avoid such artifacts?

James

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