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AMBER Archive (2007) - Re: AMBER: Binary file curiosities

AMBER 9.0 provides the option of writing trajectory files in a binary format "based on the netCDF binary file format". Can VMD 1.8.4 read and understand this new format of AMBER trajectory files, and if so, what option do I choose when I tell VMD the file type? Thank you very much for any information. Kenley

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AMBER Trajectory NetCDF Convention. Beginning with AMBER 9, a binary file format for trajectory data based on NetCDF is supported by sander, pmemd and ptraj. This format is supported by VMD beginning with version 1.8.4. The AMBER Trajectory NetCDF Convention, describes the

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Dear Amber users, I would like to implement my own analysis program and one of the functions I need is to be able to read in binary trajectories (AMBER or CHARMM) Does anyone know how I can go about doing this? That is, what is the file format ..etc. Much Thanks! Grace ----- The AMBER Mail Reflector To post, send mail to amber.scripps.edu

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See AMBER documentation for netCDF format description. NetCDF binary trajectory files are supported by the AMBER modules sander, pmemd and ptraj. Compared to formatted trajectory files, the binary trajectory files are smaller, higher precision and significantly faster to read and write.

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> In case other AMBER users want do this this with > fortan as well, I am including a rather pointless pseudo code that should > work for reading the binpos format using a fortran compiler that supports > the "binary" form option. Thanks. I've been reluctant to use this, since (as far as I can tell, e.g.

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Hi Amber folks, I have been playing with reading the various binary AMBER trajectory data types lately, and I noticed a few things that strike me as puzzling "features" of AMBER. For instance, from what I can tell from mdwrit.f, if you choose the option NTRX=1 in sander you get an unformatted file that looks exactly like the formatted mdcrd file.

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> "features" of AMBER. For instance, from what I can tell from mdwrit.f, if > you choose the option NTRX=1 in sander you get an unformatted file that > looks exactly like the formatted mdcrd file. However, I do not see the > option to write these types of files from ptraj, only binpos binary files > are available (from my inspection of

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AMBER Archive (2007) - Re: AMBER: Binary file curiosities

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> I have been playing with reading the various binary AMBER trajectory data > types lately, and I noticed a few things that strike me as puzzling > "features" of AMBER. For instance, from what I can tell from mdwrit.f, if > you choose the option NTRX=1 in sander you get an unformatted file that > looks exactly like the formatted mdcrd file.

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No Amber parameter file needs to be generated prior to using this utility, but if an appropriate parameter/topology file is available it may be given with -partop. As in <docmark>minAmber.pl</docmarl> the location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC.

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As in minAmber.pl the location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least AMBERHOME should be set accordingly. Otherwise an attempt is made to locate the Amber binary from the search path and deduce the data directory from the binary location.