[gmx-users] SHAKEt

Sekar Ramachandran sram18 at yahoo.com
Sat Mar 11 01:26:49 CET 2006

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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