[gmx-users] protein rotation!

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Wed May 21 09:52:01 CEST 2003


Ok, to get this over with, I'll summarize evrything once more.

Protein rotation can indeed be a problem when using a rectangular or 
many other triclinic boxes since the protein might well encounter its 
own image screwing up the simulation.

When doing a vacuum simulation the solution is trivial, and can be used 
in all Gromacs versions I know of, by setting comm_mode = Angular in the 
.mdp file.

For a simulation in solvent it is less trivial but feasible as was shown 
by Andrea Amadei and coworkers. They devised a method which constrains 
roto-translational movements of a solute, described in J. Chem. Phys. 
112(1) pp. 9-23.

They've implemented the method in Gromacs and a patch can be obtained 
from Danilo Roccatano ( roccata at caspur dot it ) from that group. We 
will be trying to implement things properly into Gromacs in the near 
future here in Groningen, but it has to wait a bit. If it's done we'll 
put it forward for a future release.

For now, that's that!
Hope it helps :)



David wrote:

>On Wed, 2003-05-21 at 07:06, Jinzhi Tan wrote:
>>Dear Sir:
>>If I use the version of 3.1.4, can I solve the protein rotation? If so, what parameter can achieve this? Thank you very much!
>comm_mode = ANGULAR
>or something like that. You should only do it in vacuum.

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