RE: Error applying PME to simulation set up

From: Norman Geist (
Date: Wed May 13 2015 - 05:08:45 CDT

This most likely isn't related to PME, but two other options are possible:


1. You cutoff value is close to the periodic cell size.

2. You do NPT and the box shrinks very much. Try setting "margin 5"


You might to post your namd input so we can see whats going on.


Norman Geist.


From: [] On Behalf
Of Sourav Ray
Sent: Wednesday, May 13, 2015 11:25 AM
Subject: namd-l: Error applying PME to simulation set up




I tried running a helical protein structure equilibriated in water and
ionized to 0.1 mol/L with NaCl. However, I encountered an 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."


while applying PME electrostatics whereas setting a dielectric value to say
15 is working fine.


Can anyone here provide certain insight into this issue?




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