[AMBER] MD simulation parameters: urgent please

From: Mary Varughese <maryvj1985.gmail.com>
Date: Mon, 1 Jul 2013 22:27:29 +0530


About a DNA - ligand simulation (the particular DNA ligand sytem is not
very much stable also)

in the production dynamics(in NPT):
when ntb=2, ntp=1, pres0=1.0, ntt=3

1: what should be the appropriate value of gamma_ln ? (i have used 1 )
does increasing value to 5.0 has any advantage
2: also what is the significance of taup=2.0 ; how does it affect the
3: also should i essentiallly include ig=-1 as it says in amber DNA
tutorials in the case of ntt=3.
4: Also i hope adding these values doesnt affect mmpbsa calculations.

5: Also sir does iwrap=1 has any influence on mmpbsa calculations?

Thanking you

Mary Varughese
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Received on Mon Jul 01 2013 - 10:00:03 PDT
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