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.
Sekar Ramachandran wrote:
> I am using SHAKE to constrain bonds during my
> 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.
> Sekar Ramachandran
> Research Associate
> 316 Baker Laboratories
> DEpartment of Chemistry and Chemical Biology
> Cornell University
> Ithaca 14853
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