Hi Voytek,
You can also edit mdin_ctrl_dat.F90 in the src/pmemd/src directory and change
integer, parameter :: gridhi = 512
to
integer, parameter :: gridhi = 1024
Then recompile and I believe this should just work. It will up the memory requirements in places but it should be fine. This should carry over into the GPU code as well although I didn't look in detail but I don't see any reason why a larger FFT shouldn't work. It may not be optimal from a performance standpoint but I think it shouldn't cause any issues.
All the best
Ross
> On Mar 30, 2016, at 13:08, Kasprzak, Wojciech (NIH/NCI) [C] <kasprzaw.mail.nih.gov> wrote:
>
> 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 - 13:30:04 PDT
