restart file

From: Constantin Gunkel (alanka_at_hotmail.de)
Date: Fri Oct 30 2020 - 09:45:17 CDT

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@Peter Freddolino

Thanks for the quick answer.

Here is the first restart file. The rest look all the same, just
importing the information of the last restart outputs and not the
original one. I have also tried them without the extra new minimization
steps below but nothing really works.

Best,

Constantin

# input
set input               ../hoffnung/SI.restart
coordinates             ${input}.coor
velocities              ${input}.vel
extendedSystem          ${input}.xsc
structure               ../hoffnung/SI.psf
parameters              ../hoffnung/par_all36_prot.prm
parameters              ../hoffnung/par_all36_na.prm
parameters              ../hoffnung/par_all36_lipid.prm
parameters              ../hoffnung/par_all36_carb.prm
parameters              ../hoffnung/par_all36_cgenff.prm
parameters              ../hoffnung/toppar_water_ions_namd.str
paratypecharmm          on

# output
set output              ../hoffnung/SI1
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 10000
xstFreq                 10000

binaryoutput            no
binaryrestart           no
outputEnergies          100
restartfreq             1000

fixedAtoms              off

# Basic dynamics
exclude                 scaled1-4
1-4scaling              1
COMmotion               no
dielectric              1.0

# Simulation space partitioning
switching               on
switchdist              9
cutoff                  10
pairlistdist            12

# Multiple timestepping
firsttimestep           475000
timestep                2
rigidBonds              all
stepspercycle           20
nonbondedFreq           2
fullElectFrequency      4

# Temperature control

set temperature         325

# Langevin Dynamics
langevin                on;            # do langevin dynamics
langevinDamping         1;              # damping coefficient (gamma) of
1/ps
langevinTemp            $temperature;   # bath temperature
langevinHydrogen        no;             # don't couple langevin bath to
hydrogens
seed                    12345

# Pressure control
langevinPiston          on
langevinPistonTarget    1.01325; # in bar -> 1.01325 bar = 1 atm
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      $temperature
useFlexibleCell         no
useGroupPressure        yes
fixedAtomsForces        off

# PBC
wrapAll                 on
wrapwater               on
dcdUnitCell             yes

PME                     yes
PMEGridSizeX            120
PMEGridSizeY            120
PMEGridSizeZ            150

# Extra Parameters

margin 3

# Scripting
minimize            40000

run                 400000

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