run NPT equilibration

From: Wen Li (liw_at_wadsworth.org)
Date: Tue Feb 08 2005 - 11:30:07 CST

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I am trying to run an MD equilibration at constant pressure. I wonder if
the following setting for configuration file would do it:

amber yes
parmfile myAmberParam.top
readexclusions off
ambercoor myAmberRestart.rst
outputname test_nmad

rigidBonds all
timestep 2
useGroupPressure yes
useFlexibleCell yes
#langevinPiston on
langevinPistonTarget 1.013
rigidTolerance 0.0005
numsteps 1000

outputEnergies 100
restartfreq 100
DCDfreq 100

exclude scaled1-4
1-4scaling 0.83333
temperature 300
cutoff 12
switching off

PME on
cellBasisVector1 80.1563 0.0 0.0
cellBasisVector2 0.0 78.6237 0.0
cellBasisVector3 0.0 0.0 74.9825
cellOrigin 0.0 0.0 0.0

PMEGridSizeX 80
PMEGridSizeY 80
PMEGridSizeZ 80

Thanks,
Wen

• Next message: Hrant Gharabekyan: "Question about Constraint failure in RATTLE algorithm for atom"
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• In reply to: Wen Li: "Re: question on running NAMD2 using Amber files"
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