[gmx-users] Molecular Dynamics in a methane box

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 15 16:08:04 CET 2005

Nunez, Sara wrote:
> 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? 

maybe you want to copy the vdwradii.dat file and make a special entry 
for your solvent there, increase the radius to prevent collisions.

> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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