Re: about md in npt

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Wed Dec 28 2011 - 07:55:02 CST

Hi Hasan,

An basic question to clarify is how does the pressure change as a function of time. If your system was prepared from from the equilibrium density at your given target pressure, there is going to be some initial large fluctuations as the system relaxes. What is the average pressure over the last 1 ns? Is it significantly different than over the first ns?

Also looking at your config file, in case you just copied values from someone else's example, you should think about whether you want ConstantArea turned on, and whether you want to use "useFlexibleCell", for what I imagine is an isotropic system.

Best wishes,
Josh

On Dec 28, 2011, at 3:18 AM, Hasan haska 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

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