Fwd: all atom equilibrium of yeast PGK simulation with NAMD

From: Qing Li (ql29_at_duke.edu)
Date: Tue Feb 03 2015 - 21:14:36 CST

*I am trying to do all atom thermo equilibrium simulation of yeast PGK
(PDB: 3PGK). I built the solvated and ionized psf and pdb model based on
3PGK. I used the following .namd file to set up the simulation.*

set temperature 310
set outputname eq1
set inputname eq1

firsttimestep 0

# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_na_lig.prm
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333333333
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 1.0
rigidBonds water ;
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
if {1} {
cellBasisVector1 89.9 0.0 0.0
cellBasisVector2 0.0 82.6 0.0
cellBasisVector3 0.0 0.0 109.2
cellOrigin 24.0 -9.5 7.7
wrapAll on
margin 3

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile cut_1TIT_solvated_ions_minim_constrained.ref
fixedAtomsCol B

# Output
outputName $outputname

restartfreq 10000 ;# 500steps = every 1ps
dcdfreq 5000
xstFreq 5000
outputEnergies 500
outputPressure 500

Constraints no
ConsExp 2
ConsRef backbone_res.pdb
ConsKFile backbone_res.pdb
ConskCol B

# Minimization
minimize 5000
reinitvels $temperature

run 3000000;# 3ns

*After it ran for about 5000 steps, it stopped running and showed the
following error message:*
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.

*Then I turned the lagevinPiston off to do NVT ensemble. It then showed the
following error message and stopped running again:*
Error: Margin is too small for 3 atoms during timestep 7369
Error: Incorrect nonbonded forces and energies may be calculated!

*I don't know what else I can try to fix the simulation.*

*When I built the PSF model 3PGK.pdb, I used molecule dimensions and box
padding min and max both of value 30 for all 3 dimensions. Then I ionized
the model with 0.15 mol/L NaCl concentration*

Best Regards
Yours sincerely
Qing Li
PhD candidate
Department of MEMS
Duke University

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