²é¿´: 2359  |  »Ø¸´: 10
µ±Ç°Ö»ÏÔʾÂú×ãÖ¸¶¨Ìõ¼þµÄ»ØÌû£¬µã»÷ÕâÀï²é¿´±¾»°ÌâµÄËùÓлØÌû

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
»Ø¸´´ËÂ¥

» ²ÂÄãϲ»¶

» ±¾Ö÷ÌâÏà¹Ø¼ÛÖµÌùÍÆ¼ö£¬¶ÔÄúͬÑùÓаïÖú:

» ÇÀ½ð±ÒÀ²£¡»ØÌû¾Í¿ÉÒԵõ½:

²é¿´È«²¿É¢½ðÌù

ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

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¤

¸Ä³ÉÕâÑùÊÔÊÔ
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.

̫С¡£¸Ä´ó¡£

ug½¨ÒéµÄÊÇ200¡¢100.ʵ¼ÊÉÏ¿ÉÄÜÐèÒª¸ü´ó¡£
4Â¥2010-12-03 16:52:48
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
×î¾ßÈËÆøÈÈÌûÍÆ¼ö [²é¿´È«²¿] ×÷Õß »Ø/¿´ ×îºó·¢±í
[¿¼ÑÐ] 307Çóµ÷¼Á +3 ÀäóÏ123 2026-03-17 3/150 2026-03-18 09:55 by macy2011
[¿¼ÑÐ] 293Çóµ÷¼Á +11 zjlµÄºÅ 2026-03-16 16/800 2026-03-18 08:10 by zhukairuo
[¿¼ÑÐ] Ò»Ö¾Ô¸Ìì½ò´óѧ»¯Ñ§¹¤ÒÕרҵ£¨081702£©315·ÖÇóµ÷¼Á +7 yangfz 2026-03-17 7/350 2026-03-17 23:57 by ÐÇ¿ÕÐÇÔÂ
[¿¼ÑÐ] 303Çóµ÷¼Á +3 î£08 2026-03-17 5/250 2026-03-17 22:01 by î£08
[¿¼ÑÐ] 268Çóµ÷¼Á +7 ºÃÔËÁ¬Ã಻¾ø 2026-03-12 8/400 2026-03-17 20:28 by xilongliang
[¿¼ÑÐ] 301Çóµ÷¼Á +4 A_JiXing 2026-03-16 4/200 2026-03-17 17:32 by ruiyingmiao
[¿¼ÑÐ] 290Çóµ÷¼Á +3 p asserby. 2026-03-15 4/200 2026-03-17 16:35 by wangkm
[¿¼ÑÐ] 211±¾£¬11408Ò»Ö¾Ô¸ÖпÆÔº277·Ö£¬ÔøÔÚÖпÆÔº×Ô¶¯»¯Ëùʵϰ +6 Losir 2026-03-12 7/350 2026-03-17 12:09 by danranxie
[¿¼ÑÐ] 271Çóµ÷¼Á +12 ÉúÈçÏÄ»¨¡­ 2026-03-11 14/700 2026-03-17 10:56 by lovewei0727
[¿¼ÑÐ] Ò»Ö¾Ô¸£¬¸£ÖÝ´óѧ²ÄÁÏר˶339·ÖÇóµ÷¼Á +3 ľ×ÓmomoÇàÕù 2026-03-15 3/150 2026-03-17 07:52 by laoshidan
[¿¼ÑÐ] 283Çóµ÷¼Á +10 С¥¡£ 2026-03-12 14/700 2026-03-16 16:08 by 13811244083
[¿¼ÑÐ] 070303 ×Ü·Ö349Çóµ÷¼Á +3 LJY9966 2026-03-15 5/250 2026-03-16 14:24 by xwxstudy
[¿¼ÑÐ] ²ÄÁÏÓ뻯¹¤Ò»Ö¾Ô¸Äϲý´óѧ327Çóµ÷¼ÁÍÆ¼ö +7 Ncdx123456 2026-03-13 8/400 2026-03-16 12:15 by karry wen
[¿¼ÑÐ] 326Çóµ÷¼Á +3 mlpqaz03 2026-03-15 3/150 2026-03-16 07:33 by Iveryant
[¿¼²©] ¶«»ªÀí¹¤´óѧ»¯²Äרҵ26½ì˶ʿ²©Ê¿ÉêÇë +6 zlingli 2026-03-13 6/300 2026-03-15 20:00 by ryzcf
[¿¼ÑÐ] 085601²ÄÁϹ¤³Ì315·ÖÇóµ÷¼Á +3 yang_0104 2026-03-15 3/150 2026-03-15 10:58 by peike
[¿¼ÑÐ] ²ÄÁϹ¤³Ì327Çóµ÷¼Á +3 xiaohe12w 2026-03-11 3/150 2026-03-14 20:20 by ms629
[¿¼ÑÐ] Ò»Ö¾Ô¸¹þ¹¤´ó²ÄÁÏ324·ÖÇóµ÷¼Á +5 ãÆÐñ¶« 2026-03-14 5/250 2026-03-14 14:53 by ľ¹Ï¸à
[¿¼ÑÐ] ²ÄÁÏÓ뻯¹¤£¨0856£©304ÇóBÇøµ÷¼Á +6 Çñgl 2026-03-12 7/350 2026-03-13 23:24 by Çñgl
[¿¼²©] ¸£ÖÝ´óѧÑî»ÆºÆ¿ÎÌâ×éÕÐÊÕ2026Äêרҵѧλ²©Ê¿Ñо¿Éú£¬2026.03.20½ØÖ¹ +3 Xiangyu_ou 2026-03-12 3/150 2026-03-13 09:36 by duanwu655
ÐÅÏ¢Ìáʾ
ÇëÌî´¦ÀíÒâ¼û