Periodic cell has become too small for original patch grid!‏

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Sep 29 2011 - 23:52:39 CDT




 Dear NAMD Users:
 
  I am working with a dppc lipid bilayer with a cationic peptid in water. I built the system using preequilibrated dppc bilayer and peptide (they both were equilibrated separately). Dppc+water and peptide pdb file were merged taking care of appropriate orientation and position for the peptide. Overlapping water molecules were deleted using:
 
set del1 [atomselect $dppc_bact "water and same residue as {water and within 2 of protein}"]
  set seg1 [$del1 get segid]
  set res1 [$del1 get resid]
  set name1 [$del1 get name]
 for {set i 0} {$i < [llength $seg1]} {incr i} {
 delatom [lindex $seg1 $i] [lindex $res1 $i] [lindex $name1 $i]
   }
 writepsf bact_dppc_temp1.psf
 writepdb bact_dppc_temp1.pdb
 
 
Finally the system was ionized in order to get a cero net charge.
 
 
The system was equilibrated (NPT ensemble) directly using files obtained with the process mentioned above, but the following error appeared during the process:

 
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.
 [0] Stack Traceback:
 [0] _ZN9HomePatch14positionsReadyEi+0x6e [0x8404a6e]
 [1] _ZN9Sequencer17runComputeObjectsEii+0xc3 [0x8491eb3]
 [2] _ZN9Sequencer9integrateEv+0x1074 [0x848ed88]
 [3] _ZN9Sequencer9algorithmEv+0x327 [0x848bd7b]

I also tried another method: Minimization (20000 steps), heating to 300 K (20000 step) and equilibration (1 ns). I had no problems neither at system minimization nor at system heating. But
when I was running sytem equilibration it appeared the same mistake: FATAL ERROR: Periodic cell has become too small for original patch grid!

 
 I have tried some solutions:
 
 1) I increased margin to 1, 2, 3, 5 and 8
 2) Also I disabled useFlexibleCell in the simulation
 
 But none of them worked.
 
 Also I looked at dcd output file using VMD and there is nothing unusual in the vizualization. I checked the log output file and there is no critical increasing or decriasing of energy. It seems a pretty normal equilibration process.

 
I used the following configuration file for the equilibration:

structure bact_dppc_90_1.psf
coordinates bact_dppc_90_1.pdb
bincoordinates bact_dppc_90_1_cal300.coor
binvelocities bact_dppc_90_1_cal300.vel
set outputname bact_dppc_90_1_eq
firsttimestep 0

paraTypeCharmm on
parameters par_lipid27.rtf
parameters par_all27_prot_lipid.prm

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
margin 2.5
 
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
 
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 100
PMEGridSizeY 80
PMEGridSizeZ 84

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 1/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
 
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp 300
 
# Output
outputName $outputname
dcdfreq 1000
outputEnergies 100

# Boundary conditions
extendedSystem bact_dppc_90_1_cal300.xsc
wrapWater on
wrapAll on

# Restrains
fixedAtoms on
fixedAtomsFile dppc_bact_90_1_restr.pdb ### Three atoms (CA of three aminoacids) positions were restrained in order to forbid peptid motion during equilibration
fixedAtomsCol B
fixedAtomsForces on

# Equilibración
run 1000000
 
 
 
 
 
 I wait someone could help me with some solution.
 
 
 Thank a lot.
 
 
 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/


                                                

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