Fwd: about md in npt

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Wed Dec 28 2011 - 02:54:01 CST

 Hi Hasan,

the volume is fluctuating too much, so the pressure of liquid is also
fluctuating a lot.

Boyang

 On Wed, Dec 28, 2011 at 4:18 PM, Hasan haska <hasanhaska_at_yahoo.com> wrote:

> Dear Namd users,
> I run a 5 ns md simulation in NPT ensamble for 1114 glycol molecules to
> equilibrate the molecules. After the md simulation I looked over the
> pressure with namdplot and saw that pressure fluctuates between 310743.7
> and -1800.41 atm and the averaged fluctuated pressure value is 720 atm
> which is too high although the target pressure is 1 atm. What is the reason
> for this ?
> Could you please make an explanation about this issue ?
> Thank you very much for your attention.
> Best regards.
>
> #--- This is a test namd configuration file
> paratypeCharmm on
> parameters gyloPRM.prm
> structure ETG.psf
> coordinates ETG_.pdb
> outputName ETGaa1_1out
> set temperature 300
> temperature $temperature
> firsttimestep 0
> # Integrator Parameters
> timestep 1
> nonbondedFreq 1
> fullElectFrequency 5
> stepspercycle 10
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.8333333
> cutoff 19.7
> switching on
> switchdist 17
> pairlistdist 24
> # Constant Temperature Control nvt
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen on ;# don't couple langevin bath to hydrogens
> #--- PBC
> cellBasisVector1 40. 0.0 0.0
> cellBasisVector2 0.0 40. 0.0
> cellBasisVector3 0.0 0.0 65.
> #--- PME
> dielectric 1
> PME on
> PMEGridSizeX 45
> PMEGridSizeY 45
> PMEGridSizeZ 72
>
> # Constant presssure Control (variable volume)
> useGrouppresssure no ;# needed for 2fs steps
> useFlexibleCell yes
> useConstantArea yes ;#
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
> #--- Output & ETGtart
> binaryoutput no
> binaryrestart yes
> restartname ETG_1outrestart
> DCDfile ETG_1out.dcd
> ETGtartfreq 1250
> dcdfreq 1250
> xstFreq 1250
> outputEnergies 1250
> forceDCDfreq 1250
> outputpresssure 1250
> outputtiming 1250
>
> minimize 12500
> reinitvels $temperature
>
> run 5000000
>

-- 
Boyang Wang, Ph.D.
-- 
Boyang Wang, Ph.D.

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