NAMD时出现了报错

lusandan

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？

lusandan

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。。。

shwfzmnltmlc

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

lusandan

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
fullElectFrequency  2  
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     0.0  66.0   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
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
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