From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jul 27 2015 - 02:32:33 CDT
Please also report
1. Error message
2. Namd version
One major problem could be you setting all those options, which are usually
fine as default.
You don’t need to set:
useConstantRatio
useflexiblecell
useConstantArea
vdwForceSwitching
splitpatch
hgroupcutoff
pairlistsPerCycle
strainrate
usegrouppressure
PMETolerance
PMEInterpOrder
rigidtolerance
rigiditerations
You should set:
timestep 2.0
numsteps 50000000
structure ../scr/final2_slp4.psf
paraTypeCharmm on
coordinates ../scr/equilibration/equil4.coor
velocities ../scr/equilibration/equil4.vel
extendedsystem ../scr/equilibration/equil4.xsc
outputname ../scr/production/prod1
outputenergies 1000
outputtiming 1000
outputpressure 1000
XSTFreq 1000
dcdfreq 1000
restartfreq 10000
binaryoutput no
binaryrestart yes
cutoff 10
stepspercycle 20
switching on
switchdist 9
pairlistdist 12
langevin on
#langevintemp 310.0
langevintemp 298.0
langevindamping 1.0
langevinpiston on
langevinpistontarget 1
langevinpistondecay 100
langevinpistonperiod 200
langevinpistontemp 298
margin 4: #<------- INCREASE DEPENDING ON INITIAL
DENSISTY FOR 1ST SHRINK
# PME
PME yes
PMEGridSpacing 1.0
fullelectfrequency 2
nonbondedfreq 1
# SHAKE/RATTLE
rigidbonds all
# 1-4's
exclude scaled1-4
1-4scaling 1.0
parameters ../lib/par_all36_prot.prm
parameters ../lib/toppar_water_ions.str
Mit freundlichen Grüßen
Norman Geist.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Merrill, Dante
Sent: Friday, July 24, 2015 8:14 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Patch-size Error (not like the other ones)
Hello,
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.
Best,
Dante
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
# INPUT
#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
# OUTPUT
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
# CUT-OFFs
vdwForceSwitching on
splitpatch hydrogen
hgroupcutoff 3.0
stepspercycle 10
switching on
switchdist 11.0
cutoff 12.0
pairlistdist 20.0
pairlistsPerCycle 2
# H-MATRIX
# CONSTANT-T
langevin on
#langevintemp 310.0
langevintemp 298.0
langevindamping 1.0
# CONSTANT-P
langevinpiston on
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 50
#langevinpistontemp 310
langevinpistontemp 298
strainrate 0. 0. 0.
usegrouppressure yes
# PME
PME yes
PMETolerance 10e-5
PMEInterpOrder 4
PMEGridSpacing 1.0
# MULTIPLE TIME-STEP
fullelectfrequency 2
nonbondedfreq 1
# SHAKE/RATTLE
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
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