| ²é¿´: 2360 | »Ø¸´: 10 | |||
| µ±Ç°Ö»ÏÔʾÂú×ãÖ¸¶¨Ìõ¼þµÄ»ØÌû£¬µã»÷ÕâÀï²é¿´±¾»°ÌâµÄËùÓлØÌû | |||
[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 |
» ²ÂÄãϲ»¶
Ò»Ö¾Ô¸Ìì½ò´óѧ»¯Ñ§¹¤ÒÕרҵ£¨081702£©315·ÖÇóµ÷¼Á
ÒѾÓÐ8È˻ظ´
0703»¯Ñ§µ÷¼Á
ÒѾÓÐ3È˻ظ´
²ÄÁÏ£¬·ÄÖ¯£¬ÉúÎ0856¡¢0710£©£¬»¯Ñ§ÕÐÉúÀ²
ÒѾÓÐ9È˻ظ´
Ò»Ö¾Ô¸Öйúº£Ñó´óѧ£¬ÉúÎïѧ£¬301·Ö£¬Çóµ÷¼Á
ÒѾÓÐ3È˻ظ´
280Çóµ÷¼Á
ÒѾÓÐ4È˻ظ´
0703»¯Ñ§µ÷¼Á £¬Áù¼¶Òѹý£¬ÓпÆÑоÀú
ÒѾÓÐ9È˻ظ´
¹¤¿Æ²ÄÁÏ085601 279Çóµ÷¼Á
ÒѾÓÐ6È˻ظ´
070300»¯Ñ§319Çóµ÷¼Á
ÒѾÓÐ5È˻ظ´
ÉúÎïѧ071000 329·ÖÇóµ÷¼Á
ÒѾÓÐ3È˻ظ´
0703»¯Ñ§µ÷¼Á
ÒѾÓÐ6È˻ظ´
» ±¾Ö÷ÌâÏà¹Ø¼ÛÖµÌùÍÆ¼ö£¬¶ÔÄúͬÑùÓаïÖú:
¹ØÓÚ³¬¼¶¼ÆËã»úµÄ°²×°È¨ÏÞÎÊÌ⣺²»ÄÜÓÃsudoÃüÁ¸ÃÈçºÎÊǺã¿
ÒѾÓÐ18È˻ظ´
word²Î¿¼ÎÄÏ×-βעÒýÓ㬳öÁ˵ãÎÊÌ⣬Çó¸ßÊÖ½â´ð
ÒѾÓÐ3È˻ظ´
ǩ֤ʱÓÃÉí·ÝÖ¤µÄÎÊÌâ
ÒѾÓÐ12È˻ظ´
1,3-¶þôÊ»ù»¯ºÏÎïµ¥µâ´úµÄÎÊÌâ Çë×ö¹ýÀàËÆ·´Ó¦µÄÖ¸½ÌÏÂ
ÒѾÓÐ5È˻ظ´
¡¾ÇóÖú¡¿ÔÚNAMDÔËÐÐÖÐʹÓÃCHARMM¸ñʽµÄÁ¦³¡Îļþ£¬µ«Á¦³¡²ÎÊýÀ´×ÔAMBERÁ¦³¡£¬»á³öÎÊÌâÂ
ÒѾÓÐ4È˻ظ´
¡¾ÇóÖú¡¿×öNAMDµÄ1K4C.pdbʱºò³öÏֵĴíÎó
ÒѾÓÐ30È˻ظ´
¡¾ÇóÖú¡¿GromacsºÍNAMD±ÈAmber¿ìºÜ¶àÂð£¿ÈçºÎÑ¡Ôñ£¿
ÒѾÓÐ7È˻ظ´
¡¾×¨¼Ò»áÕï¡¿bay ÌÖÂÛnamd,gmx´¦ÀíË®ÈÜÒº,µ°°×µÈMD Ä£Äâ;ÌÖÂÛË®¼°Ë®Í¨µÀ
ÒѾÓÐ50È˻ظ´
¡¾ÇóÖú¡¿NAMDºÍGromacsÄĸö¼òµ¥£¿
ÒѾÓÐ5È˻ظ´
¡¾ÇóÖú¡¿namd tutorialÓöµ½ÎÊÌâ
ÒѾÓÐ10È˻ظ´
¡¾ÇóÖú¡¿NAMD°²×°ÎÊÌâ
ÒѾÓÐ19È˻ظ´
¡¾ÔÚÏß´ðÒÉ¡¿¹ØÓÚNAMD/VMD
ÒѾÓÐ210È˻ظ´
» ÇÀ½ð±ÒÀ²£¡»ØÌû¾Í¿ÉÒԵõ½:
ÄϾ©´óѧÖÇÄÜÇý¶¯Óë¸ÐÖª²ÄÁÏʵÑéÊÒ³ÏÕв©Ê¿/˶ʿ/¿ÆÑÐÖúÀí/·ÃÎÊѧÉú
+1/279
ÎÂÖÝ´óѧÂÀ¾§¾§¿ÎÌâ×é2026ÄêÕÐÉú
+1/82
ÖØÇìÒ½¿Æ´óѧÉñ¾¿ÆÑ§ÖÐÐÄ/²¡ÉúÓëÉúÀíϵ³ÏÑûº£ÄÚÍâÓÅÐ㲩ʿ¼ÓÃ˲©Ê¿ºó¶ÓÎ飨³¤ÆÚ£©
+1/81
¸£½¨Ê¦·¶´óѧÕÐÊÕ2026Ä껯ѧ¡¢²ÄÁÏ˶ʿ3-4Ãû
+1/78
¹âѧ¹¤³Ìѧ˶µ÷¼ÁÐÅÏ¢
+2/50
»ªÄÏʦ·¶´óѧ£¨211£©²©Ê¿ÕÐÉú- µç×Ó¡¢×Ô¶¯»¯¡¢»úе¡¢ÉúÎïѧ¡¢ÎïÀíÏà¹Ø×¨Òµ
+2/38
ÕÒ¹¤×÷¾ÑéÇóÖú
+1/33
·ÄÖ¯¿ÆÑ§Ó빤³Ì¡¢²ÄÁÏ»¯¹¤·½ÏòÕÐÊÕÑо¿Éú
+1/28
±±¾©Ä³Ñо¿ÔºÉúÎﻯѧÓë·Ö×ÓÉúÎïѧÏà¹Ø×¨ÒµÉêÇ뿼ºËÖÆ²©Ê¿ÕÐÉú£¨´º¼¾£©
+1/14
ÄϾ©Ò½¿Æ´óѧ-Ĥµ°°×½á¹¹Ó빦ÄÜ¿ÎÌâ×é-ÕÐÊÕ2026¼¶²©Ê¿Ñо¿Éú
+1/11
¡¾²©Ê¿ÕÐÉú¡¿Î人¿Æ¼¼´óѧÕÐÊÕ²ÄÁÏ¡¢»¯¹¤¡¢»·¾³¡¢Ò±½ðÀà2026Äê¡°ÉêÇë-¿¼ºË¡±ÖƲ©Ê¿Éú
+1/8
¹ú¼Ò¼¶È˲ÅÍÅ¶Ó³ÏÆ¸ÉúÎïÐÅÏ¢Ïà¹Ø×¨ÒµµÄ¿ÆÑÐÖúÀí
+1/8
½ÌÓý²¿³¤½Ñ§Õߺʹ´ÐÂÍŶӷ¢Õ¹¼Æ»®¡±ÈëÑ¡ÍŶÓÕÐÊÕ ²ÄÁÏ£¬»¯Ñ§Ó뻯¹¤²©Ê¿Ñо¿Éú
+1/7
26Ä격ʿÕÐÉú
+1/6
ÉϺ£µÚ¶þ¹¤Òµ´óѧ-Öì´óº£¿ÎÌâ×éÕÐÉú£¨¹ýÏß¾ÍÄܵ÷¼Á£©
+1/5
²©ºó¼´½«³öÕ¾£¬ÇóÎȶ¨µÄ½ÌÖ°
+1/3
2026ÄêÉϺ£´óѧÍõÁÁ¿ÎÌâ×éÕÐÊÕµç´ß»¯»ò¹â´ß»¯Ñо¿±³¾°µÄ²©Ê¿Éú
+2/2
ÉîÛÚ´óѧ²ÌÐ˿ƿÎÌâ×鲩ʿºó¼°Ñо¿ÖúÀíÕÐÆ¸
+1/2
339Çóµ÷¼Á
+1/1
Öйú¿ÆÑ§ÔºµØÇò»¯Ñ§Ñо¿ËùÕпÆÑÐÖúÀí
+1/1
9Â¥2010-12-05 15:09:27
¡ï ¡ï ¡ï
zh1987hs(½ð±Ò+3):лл 2010-12-02 22:11:55
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
3Â¥2010-12-03 14:30:48
¡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
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













»Ø¸´´ËÂ¥