[gmx-users] alkane boxes

[David]

On Sun, 2003-06-08 at 12:31, aswin narain wrote:
> Could someone tell me where i can get boxes for
> hexane, heptane, octane and nonane or even better how
> to build them from pdb files.
> I have the pdb for hexane.

there is united atom decane in the share/top directory including gro and
itp. If you want protonated (for use with OPLS) you have to make them
yourself.
1. Use molden to create a single molecule
2. write topology manually
3. minimize single molecule
4. build box with genconf
5. run MD with pressure coupling for equilibration
6. check density and DHvap


> Aswin
> 
> =====
>  Aswin Sai Narain. S
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 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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