[gmx-users] hexane simulation

[David]

On Sun, 2002-12-22 at 14:31, zhangray wrote:
> 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?
It should probably work, but you will get default parameters for
everything. Better check Peter Tieleman's website (see links on
www.gromacs.org) for better params.

>  
> Thank you very much in advance!
> Any Notice is warmly welcomed!
>  
> Ray
>  
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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