On 7/04/2011 1:55 PM, ZHANG Lu wrote: > Dear all, > I am now trying to simulate crystals in Gromacs. > What I did was to convert the original crystal structure in cif format > to pdb format and then use genconf to replicate the cells and run MD. > Is it proper to do it in this way?
It's workable. Whether you need to replicate depends on the size of the periodic cell. Whether your box had enough space around the "outer" atoms is also a concern. > Because the structure I got after MD > run was completely a mess ( not like crystals any more). > Could anyone tell me the correct way to do MD simulation in crystal > environment? There are a large number of possible reasons of the problem. We simply do not have enough information to suggest anything. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
