On 18/12/2011 8:00 PM, Alex Jemulin wrote:
Dear All
I run a 1ns MD on a membrane protein and I get these values for box
coordinate's
EnergyAverageErr.Est.RMSDTot-Drift
-------------------------------------------------------------------------------
Box-X13.8670.0710.1676340.48292(nm)
Box-Y13.8670.0710.1676340.48292(nm)
Box-Z9.159290.0950.222463-0.642479(nm)
BoxX and BoxY fluctuate between 13,5 and 14,2 nm , BoxZ fluctuate
between 8,6 e 9,6 nm.
These values seem not to reach a convergence.
Which could be the cause? How can I fix it?
Does your experience of the membrane simulation literature suggest that
equilibration normally occurs over 1ns? In the absence of any
description of the starting point or procedure you used, nobody will be
able to say anything.
Mark
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