On Wed, Jan 01, 2025, PD Dr. Anselm Horn via AMBER wrote:
>
>I have a very large system with a cuboic solvent box that largely extends
>in z direction (> 1500 A) in a rod-like manner.
>When trying to run a first minimization with positional restraints via
>pmemd.cuda, I obtain the following error:
>
>| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
This is just saying that the box length along the z-direction (called "c")
must be less than 1000 Ang. You can try changing this with the "boxhi"
parameter, which is set at about line 142 in
$AMBERHOME/src/pmemd/src/mdin_ewald_dat.F90. This change may also affect
the needed value of gridhi.
I'd recommend trying short initial calculations in the CPU version. If things
look OK there, make sure the GPU version is giving results that are the same
as on the CPU. There may be changes needed in the GPU code as well to
accommodate such a large box size, but I don't think so (see below).
FWIW, I've run rod-like simulations with a box length in the long direction
of 710 Ang. without any problems (at least that I noticed!). So twice that
length is probably going to be OK. The upper limits in pmemd were
established 20 years ago or so, and probably assumed that a box length more
than 1000 Ang. was likely to be an input error.
...good luck...dac
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Received on Sat Jan 04 2025 - 21:30:03 PST
