Increase the solvent buffer to at least 12 angstom if you have a solute -
solvateoct m TIP3PBOX 12.0. And use an 8 or 9 angstrom cutoff, unless for
some reason you really need 10 (everybody I know, in worry mode, moves up to
9 from the default 8; really I don't think going above that matters that
much, given the range of things affecting ultimate accuracy). If you want
the bigger cutoff, increase the 12 even more, maybe 15. Boy, there has been
a rash of folks intent on building really small systems lately... Why set
yourself up for catastrophe? (you have to remember that the system is going
to shrink on you when you move to the NTP ensemble to get the density
right).
Best Regards - Bob Duke
----- Original Message -----
From: "Andrew Borgert" <borg0109.umn.edu>
To: <amber.scripps.edu>
Sent: Friday, July 13, 2007 12:18 PM
Subject: AMBER: Cutoff list exceeds largest sphere in unit cell
>
> Using AMBER9 on an intel linux workstation, I am running MD on a very
> small
> glycopeptide with explicit solvent, and I got the following error part way
> through the run:
>
>
>
> Cutoff list exceeds largest sphere in unit cell!!
> Big problems with imaging!!
> a,b,c = 29.3936780883931 29.3936780883931
> 29.3936780883931
> alpha,beta,gamma = 109.471219000000 109.471219000000
> 109.471219000000
> cutlist,sphere = 12.0000000000000 11.9999194351816
>
>
> The MD run has the following parameters which I have used before without
> problem:
> &cntrl
> imin=0,
> irest = 1,
> ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
> cut = 10,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 100000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
>
> The system was setup in xLeap, and water added using the following
> command:
>
> solvateoct m TIP3PBOX 9.0
>
> Any suggestions?
>
>
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Received on Sun Jul 15 2007 - 06:07:41 PDT
