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.
LIST
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