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

[David]

On Sun, 2002-12-22 at 15:04, zhangray wrote:
> 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?
just use 'atom  ' iso 'hetatm'
 
> 
> 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
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-- 
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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