[gmx-users] SHAKEt

Yang Ye leafyoung81-group at yahoo.com
Sat Mar 11 17:01:27 CET 2006

It is not indeed not an error.

Normally, we run md with step=2fs and constraints=h-bonds and LINCS (or 
SHAKE). what if we can not do so, reduce timestep to 1fs and continue. 
Further error may require check whether equilibration is sufficient.

Yang Ye

Sekar Ramachandran wrote:
> Hi,
> I am using SHAKE to constrain bonds during my
> simulations.
> If I use constraints=all-atoms, my simulations seem to
> be running fine. But, If I use constraints = h-bonds
> to constrain only hydrogen atoms attached to heavy
> atoms, my simulations seem to crash. 
> Does any one know how much of a difference does it
> make, if one uses on set over the other? Also, if it
> does, what would be the best way to correct the error?
> Thanks a lot.
> Sincerely
> Ram
> Sekar Ramachandran
> Research Associate
> 316 Baker Laboratories
> DEpartment of Chemistry and Chemical Biology
> Cornell University
> Ithaca 14853
> phone:607-254-6767
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