[gmx-users] umbrella failed

[nanyu101 at sina.com]

Dear gmx-users,  
   
     Now, I want to do some dynamics for my zinc enzyme. At the beginning, I do want to use umbrella sampling or constraint method to keep the coordination ligands of metal. I have done two tests.  
  First, I do constraint the distance between one ligand and metal cation,the running is just fine and my ppa input was listed here.  
   
  erbose           = no  
  runtype           = umbrella  
  group_1           = SUR  
  reference_group   = ZN  
  reftype           = com  
  reflag            = 1  
  constraint_direction = 0.0 0.0 0.0  
  constraint_tolerance = 0.001  
  k1                = 1000  
  pos1              = 0.0 0.0 0.0  
   
   
  Second, I do want to constraint all the distances between the coordination ligands and metal cation, but I failed. The ppa input file was listed here. I do not know the reason? The program can\\\'t read the group_2, group_3, pos2 and pos3.  
   
  erbose           = no  
  runtype           = umbrella  
  group_1           = SUR  
  group_2           = NB1  
  group_3           = NB2  
  reference_group   = ZN  
  reftype           = com  
  reflag            = 1  
  constraint_direction = 0.0 0.0 0.0  
  constraint_tolerance = 0.001  
  k1                = 1000  
  k2                = 1000  
  k3                = 1000  
  pos1              = 0.0 0.0 0.0  
  pos2              = 0.0 0.0 0.0   
  pos3              = 0.0 0.0 0.0  
   
  Thank you very much.  
   
  all your bests,  
  nanyu  

______________________________________
购惠普彩色全功能一体机送神奇四侠精美礼品( http://ad4.sina.com.cn/sina/limeng3/mail_zhuiyu/mail_zhuiyu_20051017.html )

===================================================================


注册新浪2G免费邮箱 (http://mail.sina.com.cn/chooseMode.html)