[gmx-users] Is something wrong wih my mdp?

[Kalyan Reddy]

Position restraining will restrain only the heavy atoms. Hydrogen atoms
were not included in position restraining. The frequency of vibrations of
bonds attached to hydrogen atoms is high(less than 2fs) when compared to
heavy atoms which have longer time scales(greater than 2fs). You have used
the time step of 2fs. Hence you must do...
1) apply DPOSRES for selected nucleotides using index file
2) use constraints = h-bonds.

Hope it helps!


On Tue, Apr 8, 2014 at 4:51 PM, chenxianli <1471769256 at qq.com> wrote:

> Dear Kalyan:
> Thank you so much for your reply! It's very helpful!
> However, there's still  something I wanna know. In my MD simulation ,I
> fixed
> part of RNA and relaxed the rest which I'm interested in to calculate the
> ratio . In this situation, "constraints= all-bonds" can be replaced by
> "constraints= h-bonds"?  (using the AMBER force field)
>
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-- 

Kalyan Reddy