From: Xiaoqing Wang (namdwxq_at_126.com)
Date: Wed Apr 13 2005 - 03:38:33 CDT
Hi all,
After 200000steps restrained MD simulation successfully, I performed
MD simulation but the error message appears :
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.
The system is protein+membrane+water.
The attechment file md.in is my input file.
Could anyone give me help!
Thanks in advance
-- --Xiaoqing Wuhan University Wuhan 430072 China
#forcefield
paratypecharmm on
parameters /home/wxq/study/sent/par_all27_prot_lipid_mod.inp
#molecules
structure na_added_100_12_ace.psf
coordinates na_added_100_12_ace.pdb
bincoordinates restr_md.coor
binvelocities restr_md.vel
extendedSystem restr_md.xsc
#temperature 310
#reassignFreq 100
#reassignTemp 25
#reassignIncr 25
#reassignHold 300
#temp & pressure coupling
langevin on
langevinTemp 310
langevinDamping 1
useGroupPressure yes
useFlexibleCell no
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 200
LangevinPistonDecay 500
LangevinPistonTemp 310
#output
outputname md1
outputEnergies 1
restartfreq 1000
DCDfreq 1000
binaryoutput yes
binaryrestart no
outputTiming 100
wrapAll on
wrapNearest on
#integrator
timestep 1
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 9
switching on
switchdist 8
pairlistdist 11
margin 0
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
PME on
cellBasisVector1 110.051 0 0
cellBasisVector2 0 110.146 0
cellBasisVector3 0 0 90.927
cellOrigin 2.880 2.680 3.020
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 100
#minimize 1000
run 200000
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