fgrunewald
commented
2 years ago Hi @LHRK,
Thanks for opening the issue. Could you open it with the correct polyply repro here again. Just copy the text to a blank issue there. Meanwhile I'll have a look at the problem.
Cheers, Fabian
Hi! I am trying to construct a poly A 4000 nt DNA segment, having a spherical constraint on as well. It works for 400 nt, but I get problems with 1000 nt and up.
The main issues are box size and memory error. First I get, that the box is not large enough, hence I naively increase the box, but then I get memory error.
When trying to construct the 1000 or 4000 nt with a spherical constraint using 10 nm in radius, I get the error: "OSError: Sampling the end-to-end distance distribution yielded end-to-end distances that are larger than the box diagonal. This will not work. Please increase the box to be at least 515.8467358001363 nm."
Now if I simply increase the box size, I get memory error "numpy.core._exceptions.MemoryError: Unable to allocate 349. GiB for an array with shape (3, 2500, 2500, 2500) and data type float64". This is also the case with just 1000 nt. For 400 nt, it works fine.
Okay, fair, but I find it confusing, since I am applying the sphe0rical constraint, which is smaller than the box size. Of course it can be, that my spherical restraint is too small as well with only 10 nm radius, but for now, this I can not even test. since the errors are the same not matter the spherical constraint. Increasing the radius of the spherical constraint, do not help either. PolyA.zip
I have uploaded the files for the 4000 nt DNA string I am trying to built, along with the commands used.
Help would be appreciated! Maybe I am simply misunderstanding the building file for polyply.
Best Lisbeth