Patch-size Error (not like the other ones)

From: Merrill, Dante (
Date: Fri Jul 24 2015 - 13:14:28 CDT


I am well aware of the multitude of patch-size errors on the mailing list and I have read through the majority of them and have yet to find a good answer that fits my issue. Please just read the next paragraph and then judge whether this is like the other issues posted to the mailing list.

I am attempting to correctly equilibrate and produce a relatively small protein (~50,000 atoms) in a water box (currently ~15,000) for a total of 100 ns using 2 fs timesteps using NPT (config file for production run 1 below). I have added margin, turned Flexiblecell on and off (and its two counterparts), restarted, elongated minimization and equilibration, checked the water density (its at 0.89 g/cm^3), resolvated, moved the origin to 0,0,0 , and messed with pairlistdist and switchdist settings.

I can get through my 10,000 step minimization, and 4 200,000 step equilibrations just fine. However I cannot for the life of me get my production run to go past 6 million steps without having to restart. Which would be annoying but do able if not for the fact that after every restart my patch size decreases so by restart 4 I am getting about 200,000 steps per run.
I understand that you receive a lot of emails about this issue and I am sorry to have to add to that however I feel I have exhausted my resources in trying to figure this out myself and I humbly ask for your help with this issue. Any guidance as to how to fix this or even just elongate my runs would be greatly appreciated.

Thank you for your time and efforts.



timestep 2.0
numsteps 50000000 # 100000000fs = 100000ps = 100ns

useConstantRatio yes
useflexiblecell yes
useConstantArea no

#structure ../scr/syt1_pops_prot_final.pdb.xplor.psf
structure ../scr/final2_slp4.psf
paraTypeCharmm on

#coordinates ../scr/syt1_pops_prot_final.pdb.solv.pdb
#bincoordinates ../scr/equilibration/equil5.coor
#binvelocities ../scr/equilibration/equil5.vel
coordinates ../scr/equilibration/equil4.coor
velocities ../scr/equilibration/equil4.vel
extendedsystem ../scr/equilibration/equil4.xsc

outputenergies 1000
outputtiming 1000
outputpressure 1000
binaryoutput no

outputname ../scr/production/prod1
restartname ../scr/production/prod1
restartfreq 10000
binaryrestart yes

XSTFreq 1000

dcdfile ../dcd/prod1.dcd
dcdfreq 1000

vdwForceSwitching on
splitpatch hydrogen
hgroupcutoff 3.0
stepspercycle 10
switching on
switchdist 11.0
cutoff 12.0
pairlistdist 20.0
pairlistsPerCycle 2

langevin on
#langevintemp 310.0
langevintemp 298.0
langevindamping 1.0

langevinpiston on

langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 50
#langevinpistontemp 310
langevinpistontemp 298

strainrate 0. 0. 0.
usegrouppressure yes

PME yes
PMETolerance 10e-5
PMEInterpOrder 4
PMEGridSpacing 1.0

fullelectfrequency 2
nonbondedfreq 1

rigidbonds all
rigidtolerance 0.00001
rigiditerations 400

# 1-4's
exclude scaled1-4
1-4scaling 1.0

#parameters ../lib/par_all36_na.prm
#parameters ../lib/par_all36_lipid.prm
parameters ../lib/par_all36_prot.prm
parameters ../lib/toppar_water_ions.str

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:59 CST