[gmx-users] bond breaking

David spoel at xray.bmc.uu.se
Sun Jul 17 12:45:02 CEST 2005

On Sat, 2005-07-16 at 19:24 -0700, Albert Sun wrote:
>         Dear Users,
>         I don't know if Gromacs can simulate bond break. For example,
>         if a chain of atoms subject to pull load and it breaks after
>         the pull load reach a number.  Can Gromacs simulate this and
>         produce trr file so I can use VMD to view the bond breaking.

You can use morse potentials (using a simple grompp option will convert
your bonds to morse potentials) but it will not give an accurate bonding
energy. For that you would have to do free energy calculations.

>         Appreciate if you could advise me or pass a example file to
>         me.
>         Thanks
>         Albert
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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