[gmx-users] simulations of crystal cell possible?
tejenderthakur at india.com
Mon Nov 20 17:13:24 CET 2006
i tried to simulate some small organic crystals using gromacs. but not succeded much but i would like to share my experiences. if crystal size is very small than the cut of length you have take more than one lattice in order to do simulation i.e you have to generage the pdb with large cell.one more you have take care is the cryatal symmtry gromacs don't have provision to track symmtry but your cell dimentions(scaled here to maintain the cutoff cretria) and the angles can work well with it(no choice here).also option pbc=full is a good choice.
> ----- Original Message -----
> From: "Rongliang Wu" <wurl04 at iccas.ac.cn>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] simulations of crystal cell possible?
> Date: Sat, 18 Nov 2006 15:05:40 +0800
> hello everyone,
> does anybody know how to simulate crystal cells in gromacs?
> since the cell size has to be no smaller than twice the cutoff.
> and if cutoff is too small, the program terminates because of the thus
> caused too high energy. my cell is very small about 0.7 nm.
> Rongliang Wu
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