Re: Problem with Alchemical FEP

From: Jerome Henin (
Date: Mon Aug 07 2006 - 15:24:03 CDT


First, I strongly back Michel's suggestion of enforcing isotropic cell
fluctuations. Actually, that kind of system should almost always be run in a
cubic cell, as a compromise between efficiency and simplicity.

My other question is: how big is your water box?

By the way, did you find the solution to your xsc file problem?


On Monday 07 August 2006 12:38, L. Michel Espinoza-Fonseca wrote:
> 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.
> Michel
> 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
> >
> >
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