AMBER Archive (2009)

Subject: [AMBER] Particle-mesh Ewald method

From: Yunjie Zhao (
Date: Mon Mar 09 2009 - 04:46:15 CDT

Dear Amber users,

 Using Amber 9, I am trying to do molecular simulations in TIP3P explicit
solvent models. The RNA molecule has 12 nt, 11 Na+ were randomly placed. I
want to use particle-mesh Ewald method with a cutoff of 9 angstrom to
distinguish short-range and long-range interactions. This would be too big
for QM system, I do not want to use QM system. Can anyone tell me how to
write the input file?

 My input file:
> imin=0, nstlim=10000000,
> dt=0.002,
> ntt=1, tempi=0.1, temp0=300.0,
> ntb=1,
> ntf=2, ntc=2,
> cut=9.0,
> ifqnt=1


Yunjie Zhao
AMBER mailing list