[gmx-users] MD with constraints for part of the molecule

[Angela Liu]

Dear GROMACS developers and users,

I have some questions as a follow-up of the post:
"Non-planar phenyl rings and non-linear triple bonds".
In this post, Anton presented a solution to keep part
of the molecule constrained (fixed with respect to
internal coordinates) during energy minimizations. 

My questions are:
1) Can such a method of using dummy atoms and applying
constraints still work for molecular dynamics
simulation, so that part of the molecule can freely
move, whereas the other part is fixed in internal
coordinates?

2) Can GROMACS's SHAKE function be applied to keep
part of the molecule internally fixed using MD
simulation?

3) What special care must be taken for such
constrained MD simulation?  Maybe using small time
steps and running extra long trajectories?  What
ensemble can be run? NVT or NPT?

Thanks so much for your time and help!

Angela 


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