[gmx-users] hexane simulation
David
spoel at xray.bmc.uu.se
Sun Dec 22 13:28:53 CET 2002
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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