From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Apr 13 2005 - 11:32:17 CDT
I recommend you just to increase your margin to 5 or 10 (if the system
is really huge), for example. It should solve your problem. After your
system is equilibrated (I guess you're equilibrating) you can reduce
I hope it works,
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
Behalf Of Xiaoqing Wang
Sent: Wednesday, April 13, 2005 3:39 AM
Subject: namd-l: Periodic cell has become too small for original patch
After 200000steps restrained MD simulation successfully, I performed
MD simulation but the error message appears :
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.
The system is protein+membrane+water.
The attechment file md.in is my input file.
Could anyone give me help!
Thanks in advance
-- --Xiaoqing Wuhan University Wuhan 430072 China
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:40 CST