[gmx-users] Molecular Dynamics in a methane box

Nunez, Sara Sara.Nunez at solvay.com
Thu Dec 15 15:03:28 CET 2005

Dear gromacs users,

I want to simulate an alpha-helix in a methane box (I am currently using
the G43a2 force field in Gromacs). As far as I can tell, methane is
defined in this force field as residue CH4. I have made the methane .top
& .gro files and have so  far solvated my alpha-helix using the "genbox
-cs protein.gro -ci methane.gro" command.

Unfortunately, the solvation process was not successful as methane
molecules were also positioned inside my helix and on top of protein
bonds! As a result, subsequent minimization failed. The manual says that
gromacs initially checks for solvent-solvent and protein-solvent
overlap, but I do not see so for my model.

Any clue about what I could be doing wrong? Are my methane parameters
wrong? Do I need a pre-equilibrated methane box prior to solvation?  Is
there already an available pre-equilibrated methane box in gromacs? 


Dr. Sara Nunez
Dept. of Chemical Design and Synthesis, CAMD group
Solvay Pharmaceuticals
C.J. van Houtenlaan 36
NL-1381 CP  Weesp, The Netherlands

This e-mail is confidential.
If you are not the addressee or an authorized recipient of this message,
any distribution, copying, publication or use of this information for any
purpose is prohibited.
Please notify the sender immediately by e-mail and then delete this message.
Ce message est confidentiel.
Si vous n'etes pas le destinataire designe de ce message ou une personne
autorisee a l'utiliser, toute distribution, copie, publication ou usage a
quelques fins que ce soit des informations contenues dans ce message sont
Merci d'informer immediatement l'expediteur par messagerie electronique et
d'ensuite detruire ce message.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051215/68cb21a9/attachment.html>

More information about the gromacs.org_gmx-users mailing list