Dave,
Thank you very much for the advice. I will try the higher order and larger grid spacing equal in all
directions.
Voytek
Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research, Frederick, MD.
(301) 846 5537
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: David Cerutti [dscerutti.gmail.com]
Sent: Wednesday, March 30, 2016 3:46 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Proper nfft* parameters for a very long solvent box?
Hi Voytek,
My recommendation would be to try nfft1 = 512, and set order = 6. Then,
adjust nfft2 and nfft3 as appropriate so that the grid spacings are roughly
equal in all directions, to get about 1.44A as you said. Go for values
that are multiples of 2 and 3; 5 is OK but it sounds like your box is big
enough that whatever a factor of 5 gives you the next stop on the
Two-by-Three Express isn't far. I do not know if this will work on the GPU
implementation--last I checked the default of order=4 was enforced and
other settings were unavailable.
If you run into other problems, this sounds like a pretty big system, so
NAMD or OpenMM might be a good thing to look into. If you use desmond, I
believe that code will let you do hybrid interpolation orders, so you could
do 1.44A spacing in X with 1.0A spacings in Y and Z, then set (6, 4, 4)
interpolation order.
Generally, whatever you were doing with the default 4th order interpolation
you can do with 6th order interpolation and up to 50% larger grid spacing,
for the same level of reciprocal space accuracy. Take a real space
electrostatics cutoff of 9A or greater and you'll have no issues from the
PME.
Dave
On Wed, Mar 30, 2016 at 2:14 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Dear Amber Users,
>
> I am trying to run an SMD simulation mimicking an optical tweezer pulling
> experiment
> on an RNA structure. The solvent box required to achieve full chain
> extension is
> approximately 720 A long. Letting the program (Amber 14, pmemd.MPI) set
> the PME charge
> grid parameters leads to an error: "nfft1 must be in the range of 6 to 512"
> I can set the nfft* params in the &ewald section, but I can't specify
> anything more than 512,
> which leaves the X/nfft1 = 1.44, i.e. above the 1.0A recommended in the
> manual.
>
> Are there any work-arounds for this limit? Should I set the nfft2 and
> nfft3 to yield the
> same 1.44 A spacing for symmetry, or can those params be set to values
> yielding 1.0 A?
> What are the potential consequences of keeping the asymmetric spacing?
> Is 1.44 just suboptimal or very bad?
> Any comments and suggestions would be much welcome.
>
> Thank you in advance,
> Voytek Kasprzak
>
> Wojciech (Voytek) Kasprzak [Contractor]
> Analyst Programmer,
> Basic Science Program, Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research, Frederick, MD.
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 30 2016 - 13:30:03 PDT
