Something is wrong here. A system of that size in volume, 300 * 300 * 300
angstrom**3 is just huge! - At equilibrium water density, this should be
about 2.7 MILLION atoms - so your density is very low - 5% of normal -
something wrong here (amber formats only support up to 999,999 atoms, by the
way...). So anyway, the reason the fft dimensioning blows up is that by
default the system attempts to get an fft grid density around 1
grid/angstrom, but also checks for fft's that are just huge, and does not
allow values above 256. You can find the appropriate constant, gridhi, in
mdin_ewald_dat.fpp; later versions of pmemd have bumped this up to 512
because in multiprocessor runs it will work, and there are some large
asymmetric systems that might extend past 256 angstrom in one dimension.
But here's the deal - such a low density represents some other problem in
your setup (like maybe you did not go through leap entirely correctly in
setting up the solvent box... By the way, I suspect you are using amber 9
or earlier, not 10. PMEMD 10 allows a max of 512...
Regards - Bob Duke
----- Original Message -----
From: "Ganesh Kamath" <gkamath9173.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, March 30, 2010 1:57 PM
Subject: [AMBER] issues with pmemd
> Hi all,
>
> I have a system size of 303.4454000 303.3504000 303.3644000 box size and
> it
> has 141000 atoms with water.
> However a compiled pmemd gives me this message when trying to minimize it.
>
> | ERROR: nfft1 must be in the range of 6 to 256!
> | ERROR: nfft2 must be in the range of 6 to 256!
> | ERROR: nfft3 must be in the range of 6 to 256!
>
> I think the system size is big and need to recompile pmemd. But could
> anyone
> tell me what should I be changing in the code.
> I am using AMBER 10.
>
> thanks for your time.
>
> regards,
> ganesh
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>
>
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Received on Tue Mar 30 2010 - 11:30:03 PDT
