Hey Oliver,
I have done a similar thing with amber 7. I found the same large
fluctuations. In the end i found that this was due to amber 7 using a atom
based cut off for non-periodic conditions. This meant that charges on
residues where split across the cut off causing the instabilities. To get a
residue based cut off for non-periodic conditions you have to go back to
amber 5.
Hope that helps.
On Wednesday 12 May 2004 8:08 pm, Oliver Hucke wrote:
> Dear Amber users/developers,
>
> I am have tried to speed up my simulations by switching from a periodic
> system with PME to a non-periodic system with a cap of ~300 water
> molecules on a ligand binding site. My goal is to calculate relative
> ligand binding energies with MM-PBSA and TI.
>
> I first used a non bonded cutoff of 12A for the non-periodic system.
> This lead to fluctuations of ~1000 to 2000 kcal/mol of the electrostatic
> energy (corresponding to 10% of the total energy) preventing equilibration.
> Using a cutoff larger than my system and switching off the update of the
> non-bonded pairlist solved this problem - but now the simulations are
> significantly slower than for the periodic system (details below).
> Is this to be expected?
> Do I miss something that could speed up the simulations with the cap
> without leading to instability of the electrostatic energy?
>
> Some more details:
>
> I am using sander of AMBER8.
>
> Periodic system:
> size: 50000 atoms, truncated octahedron, cut=8A
> performance: 80ps/day (with dt=0.002)
>
> non-periodic system:
> size: 10000 atoms
> performance: 30ps/day (dt=0.002)
>
> The input for the non-periodic simulation (heating after energy
> minimization):
>
> md, warm belly to 300K
> &cntrl
> imin = 0, irest = 0, ntx = 1,
> nstlim = 20000, dt = .002,
> ntpr=100, ntwx=5000,
> ntt = 1, tempi=10.0, temp0 = 300.0, tautp=1.0,
> ntc = 2, ntf = 2,
> cut = 999., nsnb=999999, scee = 1.2,
> ntb = 0,
> ibelly = 1, ntr = 1,
> &end
> &ewald
> eedmeth=4,
> &end
> -- restraint = belly
> 5.0
> RES a z
> END
> END
> -- belly
> RES a z
> END
> END
>
> -----
>
> Best regards,
> Oliver
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Received on Thu May 13 2004 - 10:53:00 PDT
