| ²é¿´: 1784 | »Ø¸´: 5 | |||
[½»Á÷]
mdrunʱ³ö´í
|
|
mdrun -s aa.tpr -o aa.trr -c aa.gro & ³öÏÖÁËÈçϵÄÌáʾ´íÎó£º step 11: Water molecule starting at atom 180665 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 13: Water molecule starting at atom 180665 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax < 1000. Potential Energy = -3.1653622e+06 Maximum force = 9.5183238e+05 on atom 180665 Norm of force = 2.3416899e+03 ÏÂÃæÊÇÎÒµÄem.mdpÎļþ em.mdp er spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp constraints = none define = -DFLEX_SPC ; Parameters describing what to do, when to stop and what to save integrator = steep dt = 0.002 emtol = 1000.0 emstep = 0.01 nsteps = 3000 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = pme rcoulomb = 1.0 rvdw = 1.0 fourierspacing =0.12 pme_order =4 optimize_fft =yes freezegrps =Protein UNK POP freezedim =Y Y Y Y Y Y Y Y Y ÎÒÒ²³¢ÊÔÁ˸ıäem.mdpÎļþÖеÄһЩ²ÎÊý(Ö»¶ÔÒ»¸ö²ÎÊý×öÁËÐÞ¸Ä)£º 1.em.mdpÎļþÖеÄfreezegrps¸ÄΪProtein UNKÄÜÁ¿ÄܺܺõØÊÕÁ²£¬ÏÂÃæÊÇËüµÄÏÔʾ½á¹û£º Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 1678 steps Potential Energy = -4.2245720e+06 Maximum force = 9.5952905e+02 on atom 9032 Norm of force = 1.1612597e+01 2.em.mdpÎļþÖеÄemstep¸ÄΪ0.00001£¨²ÎÕÕ±ðÈ˵Ļشð), ½á¹ûÏÔʾΪ£º Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 32 steps Potential Energy = -3.0919205e+06 Maximum force = 9.1417908e+02 on atom 122811 Norm of force = 1.1197423e+02 ÕâÑùµÄ½á¹ûÓ¦¸ÃÊÇÓÐÎÊÌâµÄ°É£¬Ö»ÅÜÁË32²½¡£ 3.integrator¸ÄΪmd, ½á¹ûΪ£º Writing final coordinates. Average load imbalance: 0.2 % Part of the total run time spent waiting due to load imbalance: 0.1 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 7515.940 7515.940 100.0 2h05:15 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 63.678 3.946 0.115 208.755 gcq#290: "Oh, There Goes Gravity" (Eminem) ÇëÎÊһϣ¬ÎÒÓ¦¸ÃÔõô×ö²ÅÊǺÏÀíµÄ£¿Ð»Ð»£¡ |
» ²ÂÄãϲ»¶
µ÷¼Á310
ÒѾÓÐ11È˻ظ´
300Çóµ÷¼Á£¬²ÄÁÏ¿ÆÑ§Ó¢Ò»Êý¶þ
ÒѾÓÐ9È˻ظ´
296Çóµ÷¼Á
ÒѾÓÐ3È˻ظ´
Ò»Ö¾Ô¸Äϲý´óѧ324Çóµ÷¼Á
ÒѾÓÐ3È˻ظ´
299Çóµ÷¼Á
ÒѾÓÐ9È˻ظ´
22408 359·Öµ÷¼Á
ÒѾÓÐ6È˻ظ´
085600 ²ÄÁÏÓ뻯¹¤ 329·ÖÇóµ÷¼Á
ÒѾÓÐ12È˻ظ´
Ò»Ö¾Ô¸±±¾©»¯¹¤´óѧ²ÄÁÏÓ뻯¹¤£¨085600£©296Çóµ÷¼Á
ÒѾÓÐ14È˻ظ´
085601²ÄÁϹ¤³ÌÕÒµ÷¼Á
ÒѾÓÐ11È˻ظ´
×Ü·Ö293Çóµ÷¼Á
ÒѾÓÐ9È˻ظ´
» ±¾Ö÷ÌâÏà¹Ø¼ÛÖµÌùÍÆ¼ö£¬¶ÔÄúͬÑùÓаïÖú:
GromacsÖУ¬mdrun³ö´í
ÒѾÓÐ5È˻ظ´
ÔÚgromacsÖÐÔËÐÐmdrunÃüÁîʱ³ö´í
ÒѾÓÐ10È˻ظ´
vsap 5.2 »·¾³ºÍ±àÒëÎÊÌâ
ÒѾÓÐ14È˻ظ´
Gromacs×östeepÖ®ºó×öcg³ö´í
ÒѾÓÐ5È˻ظ´
±àÒëvasp³ö´í
ÒѾÓÐ11È˻ظ´
gromacs×öÈ«Ô×ÓÄ£Äâʱºò£¬Í»È»µ½MDÕâÒ»²½³ö´í
ÒѾÓÐ6È˻ظ´
¡¾ÇóÖú¡¿°²×°vasp³ö´í make: *** [fftmpi_map.o] ´íÎó 1¡¾Òѽâ¾ö¡¿
ÒѾÓÐ6È˻ظ´
¡¾ÇóÖú¡¿vasp°²×°±àÒë´íÎó£¬Çë´ó¼Ò°ïæ¿´ÏÂÄÇÀï³ö´íÁË¡£
ÒѾÓÐ6È˻ظ´
¡¾ÇóÖú³É¹¦¡¿Vasp 5.2.11±àÒë³ö´í
ÒѾÓÐ10È˻ظ´
¡¾ÇóÖú¡¿ÔÚ±àÒëʱ³ö´í
ÒѾÓÐ6È˻ظ´
¡¾ÇóÖú¡¿PBE0 ¼ÆËãSi¡¢GeÄÜ´ø½á¹¹
ÒѾÓÐ9È˻ظ´
» ÇÀ½ð±ÒÀ²£¡»ØÌû¾Í¿ÉÒԵõ½:
¡¾Ç¿ÍÆ£ü¿ÉÁôУ¡¿¼ÃÄÏ´óѧ²©Ê¿ºóÕÐÆ¸£¨Ë®Àû¹¤³Ì/ÌúÃÌ̼»·¾³¹ý³Ì£©
+1/286
ÊýһӢһ˶ʿµ÷¼Á£¨Ë«Ò»Á÷¸ßУ£©
+1/183
ÎåÒØ´óѧҩѧÓëʳƷ¹¤³ÌѧԺ | ÁõÓîÈ׿ÎÌâ×é µ÷¼ÁÕÐÉú
+5/95
¸ÓÄÏʦ·¶´óѧФÐ˽ÌÊÚ¿ÎÌâ×éÕÐ2026¼¶µç×ÓÐÅϢ˶ʿ 4-6 Ãû£¬»¶Óµ÷¼Á
+1/82
̫ԿƼ¼´óѧ²ÄÁÏ¿ÆÑ§Ó빤³ÌѧԺÕÐÊÕ½ðÊô²ÄÁÏÀ಩ʿһÃû
+1/82
Çൺ´óѧ¹Ì̬µç³ØÑо¿ÍŶÓÕÐÊÕ²ÄÁÏ¡¢»¯Ñ§¡¢ÎïÀíµÈ·½Ïò²©Ê¿Ñо¿Éú
+2/36
¡¾ÁÖҵרҵ˶ʿµ÷¼Á1Ãû¡¿ÖйúÁÖÒµ¿ÆÑ§Ñо¿Ôº
+1/34
¸£½¨Ê¦·¶´óѧ»·¾³Óë×ÊԴѧԺ»·¾³µç»¯Ñ§¿ÎÌâ×éÕÐÊÕ2026˶ʿ£¨º¬µ÷¼Á£©
+1/29
ÈýÏ¿´óѧ²Ä»¯Ñ§ÔºÀî¶«ÉýУ³¤ÍŶӽÓÊÕ»¯Ñ§Àà˶ʿµ÷¼Á
+1/21
ÄêнԼ32-60Íò£¡³É»áÃ÷ԺʿÍÅ¶Ó³ÏÆ¸²ÄÁÏÀíÂÛ¼ÆË㲩ʿºó£¨³¤ÆÚÓÐЧ£©
+1/15
Öйú¿ÆÑ§ÔºÉϺ£¹èËáÑÎÑо¿ËùÊ©½£ÁÖԺʿÍŶӺúƼ¿ÎÌâ×éÕÐÆ¸²©Ê¿ºó
+1/14
˫һÁ÷´óÑ§ÏæÌ¶´óѧ¡°»¯¹¤¹ý³ÌÄ£ÄâÓëÇ¿»¯¡±¹ú¼ÒµØ·½ÁªºÏ¹¤³ÌÑо¿ÖÐÐÄÕÐÊÕ²©Ê¿Éú
+1/14
Î÷°²¹¤³Ì´óѧÄÜÔ´»¯¹¤Ð²ÄÁÏÑз¢ÏîÄ¿×é½ÓÊÕ2026Äê¼ÆËã»úÀàµ÷¼ÁÑо¿Éú
+1/13
ÑĮ̀´óѧÏȽøÌÕ´É·½Ïò ÕÐÊÕ²ÄÁÏרҵµ÷¼ÁÑо¿Éú
+1/11
08¹¤Ñ§Ó¢Ò»Êý¶þ290 Èý¸ö½±Ñ§½ðÁ½¸öÊ¡Èý Ò»¸öÊ¡´´ÓÅÐã½áÏî BÇøÇóµ÷¼Á
+1/10
»¶Ó¸÷λͬѧÉêÇë²Î¼Ó°ÄÃÅ´óѧ½¡¿µ¿ÆÑ§Ñ§ÔºµÄ2026ÄêÏÄÁîÓª£¬±¨Ãû½ØÖ¹4ÔÂ12ºÅ
+1/4
Î人·ÄÖ¯´óѧȫ¹úÖØµãʵÑéÊÒÂÀÓÀ¸Ö½ÌÊÚ¿ÎÌâ×éÕÐÊÕ²ÄÁÏ¡¢»¯Ñ§¡¢ÉúÎïÏà¹Ø×¨ÒµË¶Ê¿Ñо¿Éú
+1/4
Ìì½òÒ½¿Æ´óѧ»ù´¡Ò½Ñ§ÔºÕźã¿ÎÌâ×鲩ʿºóÕÐÆ¸
+1/3
26²©Ê¿ÉêÇë
+1/2
ÉϺ£Ê¦·¶´óѧÓлú»¯Ñ§×¨ÒµÑо¿ÉúÕÐÉú
+1/1
¡ï ¡ï ¡ï ¡ï
Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû
Jfreda(½ð±Ò+5): 2011-04-18 19:08:54
zh1987hs(½ð±Ò+3): лл 2011-04-18 21:33:02
Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû
Jfreda(½ð±Ò+5): 2011-04-18 19:08:54
zh1987hs(½ð±Ò+3): лл 2011-04-18 21:33:02
|
Steepest Descents converged to Fmax < 1000 in 32 steps Potential Energy = -3.0919205e+06 Maximum force = 9.1417908e+02 on atom 122811 Norm of force = 1.1197423e+02 ÕâÑùµÄ½á¹ûÓ¦¸ÃÊÇÓÐÎÊÌâµÄ°É£¬Ö»ÅÜÁË32²½¡£ ËäȻֻÅÜÁË32²½£¬²»¹ýÄãµÄÁ¦ÒѾ»ù±¾ÊÕÁ²ÁË£¬Ó¦¸ÃûÓÐʲôÎÊÌâÁË¡£Ó¦¸Ã²»ÓÃfreegroup,Èç¹ûÒªÏÞÖÆÔ×ӵϰ£¬¿ÉÒÔ³¢ÊÔʹÓÃdefine. |
2Â¥2011-04-18 18:42:24
3Â¥2011-04-18 19:10:46
¡ï ¡ï ¡ï
Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû
Óù½£½ºþ(½ð±Ò+2): лл 2011-04-19 10:02:25
Jfreda(½ð±Ò+5): 2011-04-19 13:29:55
Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû
Óù½£½ºþ(½ð±Ò+2): лл 2011-04-19 10:02:25
Jfreda(½ð±Ò+5): 2011-04-19 13:29:55
| ¶¨ÒåÁËfreegrp¾ÍÊÇÈÃÕâ¸öÔ×Ó³¹µ×²»¶¯ÁË£¨µ±È»Ëü¿ÉÒÔ¶¨Ò岻ͬ·½Ïò£©£¬¶øÊ¹ÓÃdefineÊÇʹÕâ¸öÔ×Ó¶àÁËÒ»¸ö¶îÍâµÄÁ¦£¬Ê¹Æä±£³ÖÔÚÔÀ´µÄλÖ᣿´ÄãÏëÒª´ïµ½µÄЧ¹û°É£¬Èç¹ûʹÓÃfreegrp±¾È˾õµÃ»áÐèÒªÄ㶨ÒåµÄÕâЩÔ×ÓλÖÃÒѾƽºâÁË£¬Òª²»È»µÄ»°£¬Ä㻹ÊÇÈÃÈ˼Ҷ¯¶¯£¬µ÷ÕûϾàÀë±È½ÏºÃµã£¬ÊÖ²áÉÏ˵¶ÔѹÁ¦ñîºÏ»¹ÓÐÓ°Ïì |
4Â¥2011-04-19 09:07:48
5Â¥2011-04-19 10:53:16
6Â¥2011-04-19 13:30:13














»Ø¸´´ËÂ¥