## dynamics protocol ##PME ## (128*128*128) ## 8A cutoff ## 10^-5 space tolerance; ## 4th order spline Ewald coeff ~0.35 ## ## SHAKE; 8A cutoff for vdw; ## (2fs/step; shake 10^-8) ## NTP relaxation coeff 1.0ps paircutoff at 9A; ### want langevin and pressure to be nearly newtonian over the trajectory ### put in long time constants ################################## ### 5ps relaxation time for temp and pressure ################################## ## 500ps simulation timestep 2.0 numsteps 500 ###NN * 250*1000 firsttimestep 0 ###(NN-1) * 250*1000 amber yes parmfile ../sys.nacl.cnt.parm readexclusions yes exclude scaled1-4 1-4scaling 0.83333 ## only used to get pdb type information coordinates ../min3.coor ## actual coords and velocities and cellinfo used bincoordinates ../rst.bench.coor binvelocities ../rst.bench.vel extendedsystem ../rst.bench.xsc outputname bench binaryoutput yes margin 2.0 switching on switchdist 8.0 cutoff 10.0 pairlistdist 12.0 stepspercycle 20 fullelectfrequency 1 # shake stuff rigidbonds all ## faster algorithm for the waters usesettle on ## restart every 2ps or about 4 hours restartfreq 10000 restartsave yes binaryrestart yes restartname rst outputtiming 100 ### NTP control stuff BerendsenPressure yes BerendsenPressureTarget 1.01325 BerendsenPressureCompressibility 4.57E-5 berendsenPressureRelaxationTime 5000 BerendsenPressureFreq 1 ## B-Relaxtime is in fs so 5ps is the relaxation time cheatham used 1ps ## BPressFreq is multiple of nonbonded and fullelectric ## Langevin Dynamics of temperature control ### Damping coefficient is 1/ps ### assume 50ps damping coefficient ## then its 1/50 = 0.02 ## then 1/5 = 0.2 is 5ps relaxation langevin on langevintemp 300 langevinDamping 0.2 langevinhydrogen off ## no need since they are controlled by shake # remove initial COM motion but allow to devlop later COMmotion no PME on ## defaults to 4th order spline ## defaults to 10E-6 tolerance ### my cells are max 132 and min 90 PMEGRIDSizeX 128 PMEGRIDSizeY 128 PMEGRIDSizeZ 128 wrapall on