Problem during TMD

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Wed Jun 26 2013 - 14:59:50 CDT

Hello Everyone,

I'm doing Targeted Molecular Dynamics simulation where I'm simulating a
huge protein embedded in a lipid bilayer and during my TMD simulation I see
z side of my system keep increasing and the protein becoming the completely
disordered. I see a complete mess of all the parts of my system. Can anyone
help me what could be the problem. The TMD parameters I use in my conf file
is given below.

TMD on
TMDk 200
TMDOutputFreq 100
TMDFile real-final.pdb
TMDFirstStep 0
TMDLastStep 9000000
TMDFinalRMSD 0

Thanks,

Sundar

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