Re: Problem with Alchemical FEP

From: L. Michel Espinoza-Fonseca (
Date: Mon Aug 07 2006 - 11:38:09 CDT

Just out of curiosity, are you using an anisotropic periodic cell? You
can take a look to your input file and see if the option
"flexiblecell" is "on". Unless you're simulating a system containing a
membrane, you should disable this option. It is weird that you're
setting such a big patch and you're still getting this problem. Maybe
you should pay attention to the preparation stage of your system. This
will be my guess.


2006/8/7, Jawahar Neelankatan <>:
> Hi all,
> I'm trying to do an alchemical FEP simulation of an ion in TIP3P water. I'm
> using CHARMM parameters but I get the following error at the beginning of
> the simulation:
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> I've tried pretty much everything, from increasing the margin (up to 70) to
> tweaking the PMEGrid sizes. It always gives the same error. The odd thing is
> that if I
> delete the portion of the configuration file devoted to FEP simulation, and
> just run the simulation like a normal simulation, it works fine. Does anyone
> know how to get around this problem ?
> -Jawahar
> ________________________________
> Do you Yahoo!?
> Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:53 CST