[gmx-users] simulating hydrocarbons in water

[David van der Spoel]

Adam Fraser 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)
> 

did you use 3.3.2 ? The default and only supported FF there is OPLS. For 
GROMOS variants you can try the prodrg webserver.

> 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 
> <mailto: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).
> 
>      >
>      >
>     ------------------------------------------------------------------------
> 
>      >
>      > _______________________________________________
>      > gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please search the archive at http://www.gromacs.org/search before
>     posting!
>      > Please don't post (un)subscribe requests to the list. Use the
>      > www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>     <http://www.gromacs.org/mailing_lists/users.php>
> 
> 
>     --
>     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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
>     _______________________________________________
>     gmx-users mailing list     gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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