[gmx-users] Preparing a silicon bulk

[Kevin C Chan]

Dear Users,

I wish to simulate a Silicon bulk using Gromacs. I have created the bulk using a plugin in VMD but I found difficulties when generating a top file from this pdb file. I have tried pdb2gmx and x2top but both does not work. Gromacs tells me that although we already have parameters for SI in maybe ffnonbonded.itp, we do not have SI in the residue topology database and also ffbonded.itp. How could it be and I do appreciate if anyone could share his experience of simulating a silicon bulk in Gromacs.

Another thing, I would like to assign different charge to different SI atom in my bulk. How can I achieve this?

Thanks in advance.

Regards,



Kevin
ukevi at gmx.hk