[gmx-users] 答复: [gmx-users] hexane simulation

[zhangray]

Hello David,
      Could you please give me a sample about how to use the default
params, 
for example, how to write the the "atom" section of hexane.pdb?

I've read manual before, but I am a unapprehensive man ;( 

Thx a lot!
ray
-----邮件原件-----
发件人: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
代表 David
发送时间: 2002年12月22日 20:29
收件人: gmx-users at gromacs.org
主题: Re: [gmx-users] hexane simulation

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.