[gmx-users] hexane simulation

[zhangray]

Dear Sir or Madam:,
     I am newbie of MD,  so I want to try a simple simulation of hexane.

I construct a pdb file like this:
 
COMPND  C06ane.PDB

HETATM    1  C1  C06    1       -3.209   0.720  -0.477                
HETATM    2  C2  C06    1       -1.988  -0.200  -0.606                
HETATM    3  C3  C06    1       -0.757   0.381   0.107                
HETATM    4  C4  C06    1        0.488  -0.500  -0.077                
HETATM    5  C5  C06    1        1.709   0.069   0.662                
HETATM    6  C6  C06    1        2.967  -0.776   0.427                
...; duplicated above section 10*10*10
END   
Then append a [ C06 ] section in ffgmx.rtp
[ C06 ]
 [ atoms ]
    C1   CH3   0.000     0
    C2   CH2   0.000     1
    C3   CH2   0.000     2
    C4   CH2   0.000     3
    C5   CH2   0.000     4
    C6   CH3   0.000     5
 
 [ bonds ]      
    C1    C2
    C2    C3
    C3    C4
    C4    C5
    C5    C6
Then perform pdb2gmx, ...
Is what I am doing correct?
 
Thank you very much in advance!
Any Notice is warmly welcomed!
 
Ray
 
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