[gmx-users] How does the atom mass and atom vdw radius influence the MD simulation in GMX?

[Zhenting Gao]

Hi  gmx-users,                            

     I want to add a MN2+(manganese with 2 positive charge, not bonded ) to the Gromos96 43a1 FF library.          
      
     However, I noticed that 2 files, 'atommass.dat' and 'vdwradii.dat' are read during the making of a topology file. Need I add the atom weight and vdw radii into these 2 files?          
     How does the atom mass and atom vdw radius influence the MD simulation in GMX? 


Thanks.                     

　　　　　　　                              
　　　　　　　　　　                              

Yours sincerely,                              
Zhenting Gao                              
zhentg at 163.com                               
2004-11-3                        

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Drug Discovery and Design Center,                              
Shanghai Institute of Materia Medica,                              
Chinese Academy of Science                              
P.R. China                            
URL http://www.dddc.ac.cn/group/zhentg.htm