From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Wed Mar 03 2010 - 08:23:41 CST
Hi,
If your box is shrinking too fast (as due to the lipids rearranging around the protein for instance, or gaps closing) then you can get this kind of error.
Try running your simulation from the last restart point using the last dimensions you get in your .xst file.
(If you don't have the restart or .xst files you will have to rerun the original simulation with a higher frequency of those before you start the second job)
Regards
Elia
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of jbp087_at_gmail.com [jbp087_at_gmail.com]
Sent: Wednesday, March 03, 2010 12:48 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: error
Hello,
Currently i am trying to do membrane protein dyanamics
While doing NPT simulation, i am getting following error after some MD run.
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.
I have also tried keeping "useFlexibleCell = yes", but it is also showing error after some MD run.
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.
For NPT simulation i have kept protein backbone fixed and "fixedAtomsForces = no".
Please anybody can help me regarding this error.
Thanking you in anticipation.
JIGNESH PATEL
M.S.(Pharm.) in Pharmacoinformatics,
Center for Pharmacoinformatics,
NIPER, MOHALI,
Punjab, India.
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