[gmx-users] Re:Re: wrong bonds generate by g_x2top

[Justin Lemkul]

On 3/1/13 7:47 AM, zhhxu wrote:
> Dear Justin:
>
>   Thank you for reply.  g_x2top worked correct as you suggested  when I added "-nopbc"  option.
>
> I have other questions about graphite simulation. The top/rtp file(opls-aa) generated by g_x2top missed  improper dihedral term ,
>
> to keep a carbon in plane, whether it is better to add the missing terms in topology file or need other corrections ?
>

If you need to keep groups planar, then you need impropers.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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