Dear Hanlu,
> Now I am simulating a molecular crystal ,but after MD ,the structure
> of cell (supercell) is disintegrated . I think it is a cause lacking a
> reasonable boundary condition . I want to estiblish a periodic box
> without solvent to compute the ststic-electonic interaction to keep the
> form of crystal of supercell unchanging, so inquire mehods
> estibilishing such box .
Start by building yourself a pdb representing your crystal, I assume you can
do this already given you ran a simulation initially. Then use the setbox
command within leap to provide the box dimensions in the x, y and z
coordinates. Then save the prmtop and inpcrd and you will have them setup
for periodic simulations. You can then run your simulation with ntb=1,
constant volume or ntb=2, constant pressure.
Good luck,
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon May 23 2011 - 21:00:04 PDT
