[gmx-users] simulating hydrocarbons in water

[TJ Piggot]

Just as a note editconf will covert a pdb to a gro file

Tom

--On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser 
<adam.n.fraser at gmail.com> wrote:

> Yes I tried this and it doesn't work for me.  I get:
>
>
> Fatal error:
> Library file ffG53a6.n2t not found in current dir nor in default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
>
> Also, doesn't x2top take in a gro file?  (not a pdb)  I wrote a script
> that converts pdb to gro, and I still get the above error.
>
> -Adam
>
>
> On 10/10/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Adam Fraser wrote:
>> Hello,
>>
>> I'm very new to Gromacs, and I am interested in simulating the
>> interactions of 2 hexadecane (C16H34) molecules in water (SPC/E
>> specificall).  I've spent some time experimenting with tutorials in
>> Gromacs, but I've found little help in non-protein simulations like this
>> one.
>>
>> I've built topologies for hexadecane compatible with NAMD, so I figure I
>> should be able to do the same in Gromacs but I'm fuzzy on how to go
>> about doing so (what files to edit).  I was also hoping to get some
>> input on which forcefield would be best for this sort of system.
>>
>> I'd greatly appreciate it if someone could give me some pointers on how
>> to get started here.
>>
>> Thanks very much,
>> Adam
>>
> if you have a pdb file you can run x2top (3.3.2 only).
>
>>
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>>
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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>



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.