[gmx-users] Information about boxX,boxY e boxZ

[Mark Abraham]

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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