From: Hui-Hsu (Gavin) Tsai [contr] (tsaih_at_ncifcrf.gov)
Date: Mon May 31 2004 - 11:06:04 CDT
Hi,
I am trying to run membrane calculations with NPT ensemble.
The initial membrane structure was generated from the membrane plugin from
VMD. However, NAMD keeps on giving me these error messages:
****************************************************************
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.
------------- Processor 11 Exiting: Called CmiAbort ------------
Reason: 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.
********************************************************************
My setup for NPT calculations are as below:
langevin on
langevinDamping 10
langevinTemp 300.0
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 300.0
Is there anyone who has experience could give me some advice/comments?
Thanks.
Gavin
-------------------------------------------------
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:41 CST