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kevin8871

гæ (³õÈëÎÄ̳)


[½»Á÷] ¡¾ÇóÖú¡¿ÓÃNAMD ×öNPTÄ£ÄâÓöµ½ÏÂÃæµÄÎÊÌâ

±¾ÈËÓÃNAMD×öNPTÄ£Ä⣬Óöµ½ÁËÏÂÃæµÄÎÊÌâ
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.
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.
ÕâÊÇΪʲô£¿ÏÂÃæÊÇÎÒµÄconf file
structure         3HT_20.psf
coordinates       3HT_20_centered.pdb


set outputname     NPT file for 3 HT


#continuing a run
set inputname      nimi
binVelocities      3HT_20_mini.restart.vel
bincoordinates     3HT_20_mini.restart.coor
extendedsystem     3HT_20_mini.restart.xsc
firsttimestep      6000
numsteps           2506000


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input

paraTypeCharmm            on
parameters           ht_monomer.par
# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5



# 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     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        300
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


#PBC
wrapall                         on
cellBasisVector1    31.312999725341797    0.0   0.0
cellBasisVector2     0.0   32.558000564575195   0.0
cellBasisVector3     0.0    0   45.066001892089844
cellOrigin          -3.0093722216406604e-6 1.4230939996195957e-5 2.136936927854549e-6

wrapAll             on


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        42
PMEGridSizeY        43
PMEGridSizeZ        55


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no  ;# no for water box yes for membrane
useConstantArea       no  ;# no for waterbox, maybe for membrane

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    300


# Output
outputName          $outputname

restartfreq         2500     ;# 2500steps = every 5ps
dcdfreq             1000     ;# 1000steps = every 2ps
xstFreq             1000
outputEnergies      500
outputPressure      500


#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################


#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization

run 2500000 ;# 5ns
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leewz922

½ð³æ (СÓÐÃûÆø)


¡ï ¡ï ¡ï
zh1987hs(½ð±Ò+3):лл 2010-12-03 22:49:09
kevin8871(½ð±Ò+2): 2010-12-05 09:27:20
PME ²ÎÊýÉèÖÃÓ¦¸Ã±» 2 ¡¢3¡¢ 5Õû³ý ÇÒÉÔ´óÓÚbox±ß³¤

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PMEGridSizeX        40
PMEGridSizeY        40
PMEGridSizeZ        50
5Â¥2010-12-03 20:07:30
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
²é¿´È«²¿ 11 ¸ö»Ø´ð

leewz922

½ð³æ (СÓÐÃûÆø)


¡ï ¡ï ¡ï
zh1987hs(½ð±Ò+3):лл 2010-12-02 22:11:55
°ÑÏÂÃæÕ⼸ÐÐÈ¥µô£¬ÊÔÊÔ
cellBasisVector1    31.312999725341797    0.0   0.0
cellBasisVector2     0.0   32.558000564575195   0.0
cellBasisVector3     0.0    0   45.066001892089844
cellOrigin          -3.0093722216406604e-6 1.4230939996195957e-5 2.136936927854549e-6
2Â¥2010-12-02 20:55:35
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

kevin8871

гæ (³õÈëÎÄ̳)


ÎÒÒѾ­È¥µôÁË£¬ÎÒÏÈ×öÁËNVT£¬È»ºóÓÃNVTµÄ×öNPT£¬µ«ÊÇÎÒ×öµ½ºóÃæµÄʱºò³ö´íÁË£¬ÎҲ鿴ÁËÏ£¬ÎÒµÄboxµÄ±ß³¤±ä³ÉÁË16 16 25£¬ µ«ÊÇÎÒµÄcutoff ÊÇ12£¬ÎÒ¾õµÃ±ß³¤Ó¦¸Ã´óÓÚcutoffµÄÁ½±¶£¬ËùÒÔ×îÉÙÓ¦¸ÃÊÇ24£¬ÇëÎÊÄãÓÐʲô°ì·¨ÐÞ¸ÄÕâ¸öÂÎÒÏÖÔÚÊDz»ÖªµÀÔõôŪÁË¡£
3Â¥2010-12-03 14:30:48
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

wally8962

ľ³æ (ÖøÃûдÊÖ)


¡ï ¡ï ¡ï
zh1987hs(½ð±Ò+3):thank you 2010-12-03 17:01:47
kevin8871(½ð±Ò+2): 2010-12-05 09:27:13
langevinPistonPeriod  100.
langevinPistonDecay   50.

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