Re: [AMBER] Fw: Estiblish

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 23 May 2011 20:46:28 -0700

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
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