AMBER Archive (2005)

Subject: Re: AMBER: PMEMD limitation on NFFT

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Nov 04 2005 - 21:29:17 CST

Choon-Peng -
Since everything is dynamically allocated in pmemd, I am not aware of any
problems you will hit; just increase the limit and see what happens. The
limits are values I picked up from the sander code and did not change; I
would guess that the origin is in the volume of fft data you would have if
you had a 256**3 grid space, and machine memories have gotten larger, and
you are not pressing the limit in 3 dimensions. Sounds like an unusual unit
cell though, and a big problem. Multiple processors would be good, and a
fast interconnect to handle the volume of distributed fft data. Let me know
how it goes; I am always interested in pressing the limits on size and speed
with this stuff.
Regards - Bob Duke

----- Original Message -----
From: "Chng Choon-Peng" <choonpeng_at_cb.k.u-tokyo.ac.jp>
To: <amber_at_scripps.edu>
Sent: Friday, November 04, 2005 7:38 PM
Subject: AMBER: PMEMD limitation on NFFT

> Dear AMBER users,
>
> I'm using a very long rectangular solvent box for my simulations
> and I wish to employ PMEMD (AMBER8) for production run as it'll be
> more efficient than Sander for such a case.
>
> However, I came across this error:
>
> | ERROR: nfft1 must be in the range of 6 to 256!
>
> The box I'm using has dimensions:
> Box X = 410.713 Box Y = 93.892 Box Z = 55.886
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 432 NFFT2 = 96 NFFT3 = 60
>
> I wish to know if I can simply increase the max size in PMEMD code,
> from 256 to 512?
> (I know where to change it)
>
> Can anyone please advice?
> Thank you very much.
>
>
> regards,
> Choon-Peng
>
> --------------------------------
> Choon-Peng CHNG
> Doctoral Student (Yr 1)
> Department of Computational Biology
> Graduate School of Frontier Science
> Affiliated with
> Lab. of Molecular Design
> Room 107,
> Institute of Molecular and Cellular Biosciences
> 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
> The University of Tokyo
> Tel: +81 03-5841-1472
> http://www.iam.u-tokyo.ac.jp/MolDes/indexE.html
> ---------------------------------
>
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