NAMD时出现了报错
我运行NAMD时出现了报错ERROR: Constraint failure in RATTLE algorithm for atom 2684!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2370!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2244!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1362!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 146!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1246!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 625!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1761!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1796!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 68!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 739!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
请问有人出现过这种情况吗，最怎么解决呢？
问题我自己解决了，因为没加水盒子，另外参数设置也有问题。囧。。。 lusandan 发表于 2016-11-15 12:08
问题我自己解决了，因为没加水盒子，另外参数设置也有问题。囧。。。
我也出现了同样的问题，请问楼主修改了哪些参数，我借鉴下，谢谢了 shwfzmnltmlc 发表于 2016-11-28 20:25
我也出现了同样的问题，请问楼主修改了哪些参数，我借鉴下，谢谢了
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure mypsf.psf
coordinates mypdb.pdb
set temperature 310
set outputname myout
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0;# 2fs/step
rigidBonds all;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency2
stepspercycle 10
# 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
cellBasisVector1 61.0 0. 0.0
cellBasisVector2 0.066.0 0.0
cellBasisVector3 0.0 0 94.0
cellOrigin 5.757967472076416 8.7138090133667 -5.646048545837402
wrapAll on
# 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 no
useConstantArea no
langevinPiston on
langevinPistonTarget1.01325 ;#in bar -> 1 atm
langevinPistonPeriod100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 2500 ;# 5ps
关键就是周期性边界要比你算出来的大一点，比如算出来是68.5，参数里就写69
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