> I tried to run the same simulation using double precision on the GPU and the output seems to be fine, whereas the
Probably you mean CPU...
> single precision seems to throw a bunch of errors (coordinate overflow etc.). Of course, the simulations with
> double precision pmemd implementation runs a lot slower than what we would expect a GB simulation to run. Is there
> a way/combination of parameters in the MD input file that could be run for the single precision implementation of
> pmemd?
No, and echoing what DAC said, often instabilities at the beginning of a
simulation are due to a poor initial structure (which can be relaxed on
CPU first). Another possibility that comes to mind is that it is possible
to compile up different versions of the GPU code, for example the DPFP
(double precision / fixed precision) which is slower but can handle the
larger force variance better (likely, unless the initial structures are
really poor).
Regarding poor initial structures, we have seen peptides threaded through
aromatic rings post initial relaxation and other distortions that lead to
vdw overlap that is difficult to resolve. As per past posts, I often try
initial minimization with electrostatics turned off to relax vdw (although
this will not prevent a chain threaded through a ring).
http://archive.ambermd.org/202101/0058.html
--tec3
p.s. delayed sending this since I wanted to send picture of peptide
threaded through an aromatic from my lab, however we are not onsite that
often
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Received on Wed Nov 09 2022 - 20:30:03 PST
