| 2:01:08 AM PDT - Fri, Jul 26th 2013 |
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Dear All,
I am confused by what is the best way to setup pme parameters during molecular dynamic calculations. I have tried many different combinations on water box simulation with a small peptide in the center of the box.
I have tried pme single range of 3nm, but the system shrinks after a period of simulation. The size of the system shrinks from initially 1550nm**3 to 1400nm**3, which should be wrong.
However, if I increase the pme cutoff, the system runs much much longer.
Could someone tell me, suppose if I have a box of 7nm by 7nm by 7nm, what is the best parameterization of pme in this system?
Many thanks!!
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