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±¾ÈËÓÃNAMD×öNPTÄ£Ä⣬Óöµ½ÁËÏÂÃæµÄÎÊÌâ FATAL ERROR: Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation. FATAL ERROR: Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation. ÕâÊÇΪʲô£¿ÏÂÃæÊÇÎÒµÄconf file structure 3HT_20.psf coordinates 3HT_20_centered.pdb set outputname NPT file for 3 HT #continuing a run set inputname nimi binVelocities 3HT_20_mini.restart.vel bincoordinates 3HT_20_mini.restart.coor extendedsystem 3HT_20_mini.restart.xsc firsttimestep 6000 numsteps 2506000 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ht_monomer.par # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp 300 langevinHydrogen off ;# don't couple langevin bath to hydrogens #PBC wrapall on cellBasisVector1 31.312999725341797 0.0 0.0 cellBasisVector2 0.0 32.558000564575195 0.0 cellBasisVector3 0.0 0 45.066001892089844 cellOrigin -3.0093722216406604e-6 1.4230939996195957e-5 2.136936927854549e-6 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 42 PMEGridSizeY 43 PMEGridSizeZ 55 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no ;# no for water box yes for membrane useConstantArea no ;# no for waterbox, maybe for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp 300 # Output outputName $outputname restartfreq 2500 ;# 2500steps = every 5ps dcdfreq 1000 ;# 1000steps = every 2ps xstFreq 1000 outputEnergies 500 outputPressure 500 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization run 2500000 ;# 5ns |
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zh1987hs(½ð±Ò+3):thank you 2010-12-03 17:01:47
kevin8871(½ð±Ò+2): 2010-12-05 09:27:13
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