[gmx-users] how to simulate crystals in Gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 7 06:05:07 CEST 2011

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.


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