Problem during TMD

From: Peterson J (
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



This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:21 CST