Charm++ parallel programming system

[张笑 <xiaozhangysuniv AT 163.com>]

Dear Sir

     I am Zhang Xiao, a PHD in Beijing Institute of Technology, I have read your reply letter showed on internet tittled" Re: error during heating of the minimized system in NAMD", so I have a similar question about NPT ensemble to ask you.

      When i use NPT ensemble to control Temperature and Pressure of the system, which is a simple periodic water box. The output Temperature value is the target i set in conf. , however, the Pressure value is much more smaller (around -21000) than i set in conf.(1.01Bar).

        I am pasting my conf. below. Please let me know if there is any error in my conf. file.

#############################

#water energy minimization########

#############################

# molecular system

structure water.psf

coordinates water.pdb

set temperature         310

set outputname         water_minieng

firsttimestep          0

######### Simulation  Parameters #############

##############################################

#  Input

paraTypeCharmm        on

parameters            par_all27_prot_lipid.inp

temperature          $temperature

#  Force-Field Parameters

exclude               scaled1-4

1-4scaling            1.0

cutoff                12.0

switching             on

switchdist            10.0

pairlistdist          14.0

#dielectric            1.0           kyy files

# Integrator Parameters

timestep              1.0

rigidBonds            all

nonbondedFreq         2

fullElectFrequency    4

stepsPercycle         20

# period boundary condition

cellBasisVector1     100    0    0

cellBasisVector2      0     70   0

cellBasisVector3      0     0    30

cellOrigin           -20   -65   15

wrapAll               on

# PME alogrithm

PME                   on

PMEGridSizeX          110

PMEGridSizeY          80

PMEGridSizeZ          40

# Constant Temperature Control

langevin              on

langevinTemp          $temperature

langevinDamping       2.0

langevinHydrogen      off

#Constant Pressure Control

useGroupPressure      yes

useFlexibleCell       yes

useConstantarea       no

langevinPiston        on

langevinPistonTarget  1.01325

langevinPistonPeriod  200.0

langevinPistonDecay  100.0

langevinPistonTemp    $temperature

# Output

outputName            $outputname

#restartname           water_mine_restart

restartfreq           20000

#outputTiming         500

#outputPressure        400

DCDfile               $outputname.dcd

DCDfreq               400

velDCDfile            $outputname.veldcd

velDCDfreq            400

outputEnergies        100

outputPressure        100

xstFreq               200

####################################################################

#Execution Script  

####################################################################

minimize          1000

reinitvels        $temperature

run               400000

I am looking forward to your reply.

Thanks

--

Zhang Xiao

PhD candidate

School of aerospace and engineering 

Department of Biomechanics

Beijing Institute of Technology(BIT)

Phone Number: 13021927700

email: xiaozhangysuniv AT 163.com

张笑

	张笑
xiaozhangysuniv AT 163.com

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