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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