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Author: HeydenLabASU

demos/NAMD/ionFlux/md/150mV-2.conf

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+# NAMD config file for step 
+
+### run specific parameters
+structure                       T3_MNN.psf
+coordinates                     T3_MNN.pdb
+outputName 			150mV-2
+XSTfile 			150mV-2.xst
+
+# set up cell size or bincoordinates and extended system
+bincoordinates                 150mV.restart.coor
+binvelocities                  150mV.restart.vel
+extendedSystem                 150mV.restart.xsc # average the dimension of last 5ns pf NPT
+
+# procedure to get the first time step for the new simulation
+# from the old simulation whether it be a completed sim or one
+# to be restarted
+
+constraints                     on
+consKCol                        B
+consref                         restraint_Xray_T3_MNN.pdb # CA of protein
+consKFile                       restraint_Xray_T3_MNN.pdb
+
+#temperature controll
+langevin                        on
+langevinTemp                    295
+langevinFile                    LANGEVIN_Xray_T3_MNN.pdb #heavy atoms of lipid
+langevinCol                     B
+
+
+switching                       on
+switchDist                      10
+cutoff                          12
+pairlistdist                    13.5
+
+### common parameters
+binaryOutput                    yes
+binaryRestart                   yes
+
+parameters              par_all36m_prot.prm
+parameters              par_all36_lipid.prm
+parameters              par_all36_na.prm
+parameters              toppar_water_ions.str
+
+
+rigidBonds       all
+rigidTolerance   1.0e-8 
+
+paraTypeCharmm                  on
+wrapAll      yes
+wrapNearest  yes
+COMmotion                       no
+
+outputEnergies                  1
+outputTiming                    2400
+xstFreq                         2400
+dcdFreq                         2400
+restartFreq                     2400
+
+timestep                        2
+nonBondedFreq                   1
+fullElectFrequency              2
+
+
+# usePMECUDA on
+# SOAintegrate on
+# CUDASOAintegrate on
+# bondedCUDA 255
+
+stepsPerCycle 400
+pairListsPerCycle 40
+margin 8
+
+
+Pme                             on
+PmeGridSpacing                  1.0
+
+exclude                         scaled1-4
+1-4scaling                      1
+
+
+set zlength 83.125715709
+#z dimension of box size
+set voltage  0.15
+### electric field
+eFieldOn                        on
+eField                          0.0 0.0 [expr 23.06054917 * $voltage / $zlength]
+
+# IMD parameters
+
+# standard IMD parameters
+# IMDon streaming -- on or off
+IMDon		yes
+# IMDport -- port number to listen on
+IMDport		8895
+# IMDfreq -- frequency to send data
+IMDfreq		1
+# IMDwait -- wait for client to connect before starting simulation
+IMDwait		on
+
+# IMD version -- 2 for VMD and 3 for latest protocol
+IMDversion     3
+# IMD session info settings
+# IMDsendPositions -- sending positions of entire system
+IMDsendPositions        yes
+# IMDsendEnergies -- sending energies and bonded, non-bonded and other contributions
+IMDsendEnergies     yes
+# IMDsendTime -- sending time information (time, dt, step)
+IMDsendTime        yes
+# IMDsendBoxDimensions -- sending box dimensions (lattice vectors a, b, c)
+# If box dimensions are not defined, default unit box is sent
+IMDsendBoxDimensions       yes
+# IMDsendVelocities -- sending velocities of entire system
+IMDsendVelocities       yes
+# IMDsendForces -- sending forces on all atoms
+IMDsendForces      yes
+# IMDwrapPositions -- wrapping positions to box; applicable when IMDsendPositions is yes
+IMDwrapPositions       yes
+
+run                             144000000

demos/NAMD/ionFlux/md/150mV-2.dcd

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+# NAMD extended system configuration restart file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
+2400 65.9159773737 0 0 0 65.9159773737 0 0 0 83.125715709 0 0 0

demos/NAMD/ionFlux/md/150mV-2.restart.coor

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+# NAMD extended system configuration restart file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
+4800 65.9159773737 0 0 0 65.9159773737 0 0 0 83.125715709 0 0 0

demos/NAMD/ionFlux/md/150mV-2.restart.coor.old

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+# NAMD extended system trajectory file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
+0 65.9159773737 0 0 0 65.9159773737 0 0 0 83.125715709 0 0 0

demos/NAMD/ionFlux/md/150mV-2.restart.vel

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+# NAMD extended system trajectory file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
+0 65.9159773737 0 0 0 65.9159773737 0 0 0 83.125715709 0 0 0