[gmx-users] Molecular Dynamics in a methane box

[Nunez, Sara]

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? 

Thanks!
sara

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



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