equilibrate the system in NPT

From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Mon Dec 26 2011 - 13:57:37 CST

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 ? I attached the out file to the link . Could you please examine these files and control if there is something wrong with my md simulation ?  http://www.mediafire.com/?j08j46vump45j6y Thanks 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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