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
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Received on Wed Mar 30 2016 - 11:30:03 PDT
