VMD-L Mailing List

From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Fri Aug 12 2016 - 13:27:27 CDT

Hello All,

I have been trying to equilibrate and minimize integrin alphaVbeta3 in a
waterbox. I finished up a long equilibration simulation (about 40 ns), but
am running into the "ERROR: Constraint failure in RATTLE algorithm for atom
994!" when I try to run a constant-force simulation. After reading up on
this error, I changed the dcd frequency to every timestep and looked at the
dcd file in VMD. When looking at the dcd file, it looks as though the smd
atoms being pulled (by about 700 pN) move while every other atom stays
fixed. It seems to me (though I am far from an expert) that the energy has
not reached a constant value and therefore I would need more minimization
steps. Before the equilibration, I minimized the system with three
different minimzation simulations which were 10,000 timesteps each. My
system has about 170,000 atoms, which is very large. Would anyone know how
many minimization steps this system would need? Also, I could be on the
wrong track with what my problem is, so if anyone has any other ideas that
would be great. Thank you all for your help!

Thanks,

Jack