From: Constantin Gunkel (
Date: Wed Oct 28 2020 - 20:15:43 CDT

Hello everyone.

I have created a membrane System of 140 x 140 lipids with 4 Melittin
Peptides above. The system is solvated and neutralized. The plan was to
let it run for at least 60 ns meaning 2fs per timestep so all in all
30000000 steps with a minimization of 30000 (all NPT).  I increased the
temperature slowly every 3000 steps starting at 60 K to 325 K.

I have 2 main problems. Every now and then I get the error:

fatal error: periodic cell has become too small for original patch grid!

The error became less frequent after i used the "margin 3" command in
the config file.

Also i used the restart files to continue which helped yet the error
still happens sometimes and its still annoying. However my biggest
problem is this:
ERROR: Constraint failure in RATTLE algorithm for atom XXXX!

I used the same method as above. Restarting at the last checkpoint. I
can do about 200000-300000 steps before it crashes. However I am at
1756000 and the restart does absolutely nothing. I immediately get the
second error. If one of you could help me or maybe has a similar problem
I really would appreciate the advise. It is very import for me to get
this simulation run.

Constantin Gunkel

original config file:

# input
coordinates             ../hoffnung/SI.pdb
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/SI
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 10000
xstFreq                 10000

binaryoutput            no
binaryrestart           no
outputEnergies          1000
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           0
timestep                2
rigidBonds              all
stepspercycle           20
nonbondedFreq           2
fullElectFrequency      4

# Temperature control

set temperature         325
temperature             $temperature;  # initial temperature

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

cellBasisVector1        140 0.0 0.0
cellBasisVector2        0.0 140 0.0
cellBasisVector3        0.0 0.0 180
cellOrigin              0.6 3.46 -40
wrapAll                 on
dcdUnitCell             yes

PME                     yes
PMEGridSizeX            125
PMEGridSizeY            120
PMEGridSizeZ            160

# Extra Parameters
margin 3

# Scripting

minimize            50000
reinitvels          60
for {set t 60 } {$t <= $temperature} {incr t} {
       run 3000
       langevintemp $t
run                 3000000

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