A question on simulation with NPT ensemble

From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Fri Mar 03 2006 - 13:18:34 CST

Hi NAMD users,
    I am trying to equilibrate a solvated protein with
nearly 60 residues. I am using isothermal-isoberic
ensemble to equilibrate with periodic boundary
condition. At first, I calculated the box size using
TkConsole in VMD ( using the command measure minmax
and measure center ) and I used that to set up
cellBasisVectors and cellOrigin. After that, during
each restart I am passing xsc file saved from last
step for boxsize and boxorigin. I found that NAMD is
changing the box size slightly at each step which is
evident. Now do I need to also change the PMEGridSize
when the box size changes? Or can I keep thw samw
PMEGridSize as long as my cellBasisVectors are smaller
than PMEGridSize parameters?


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