From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Feb 16 2011 - 12:15:11 CST
Dear NAMD users,
I am getting a constant error message in my membrane simulation. If I will
imersed my protein into membrane then during melting of lipids there is no
error message and simulation goes smoothly. However, If I will do the
simulation with membrane only(melting of lipids) then it crashes everytime.
So far I did 4 diffierent trials inculding the margin option in one of the
simulation but it always gives me gfollowing error message.
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 20000
FINISHED WRITING RESTART VELOCITIES
ERROR: Constraint failure in RATTLE algorithm for atom 7948!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
Even after increasing the minimization steps to 10000, it gives me the
similar error message for different time of the simulation.
After carefully checking the atoM NAME, i found the atom is C22 from the
lipids. So there is no error from TIP3 molecule.
I will highly appreciate your help to resolve this problem. I already spend
many cpu hours to get job done.
Thanks in advance.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:50 CST