Re: [AMBER] two questions about Amber annealing

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 19 Jun 2010 21:19:50 -0700

> annealing (0K-1200K-0K)
> "Coordinate resetting (SHAKE) cannot be accomplished,

I think your temperature is pushing the force field beyond its
tolerance. There may be no reliable way to solve this, however

> I sometimes can solve this problem by dividing the annealing input
> to several files and run them one by one

This changes the trajectory slightly by truncating precision of the
coordinates and velocities. Which implies that the problem may be
avoidable by slight modification to the starting conditions for each

Possibly if you save velocities (mdvel) as well as mdcrd, you could
construct a series of restrt files by joining mdcrd[i] with mdvel[i]
in the proper restrt format. Then you could try successive files as
input for your next stage until one hopefully dodges the bullet.


AMBER mailing list
Received on Sat Jun 19 2010 - 21:30:03 PDT
Custom Search