FEP: FATAL ERROR: Periodic cell has become too small for original patch grid!

From: List (zheng042003_at_yahoo.com)
Date: Wed Mar 12 2008 - 13:29:38 CDT

Dear NAMD experts,

I have some questions about FEP (Free Energy Perturbation) and MCTI (Thermodynamic Integration). The configuration file I used is attached. Here are my questions:

1) I'm running FEP simulation in NPT ensemble. My system is a protein with a small water box enclosing the site of interest, and I'm running non-PBC FEP with atoms far away from that site fixed. According to some early posts in NAMD mailing list, I have the following settings:
     wrapAll off
    wrapNearest off
    PME no
    (All cellBasisVector1, ..., celOrigin lines have been removed)
    margin 2.5
    useFlexibleCell no

But the FEP simulation CRASHED with the following error:
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
I even tried to increase margin to a much bigger number but it didn't help. I'm not using PME/PBC, so I don't understand why it complains about the periodic cell. Could someone help?

2) I also tried NVE ensemble, but I got the message saying that FEP only works for NPT. Is this right?

3) In the FEP, I want to do thermodynamic integration, so I included the MCTI block in the configuration file AFTER the FEP specification. I wonder if this would work.

Any help will be greatly appreciated.


Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:47:37 CST