Hi AMBER community!
I'm currently attempting to simulate a protein system, with a water box,
using AMBER's temperature-based replica exchange. I am following directions
from this helpful AMBER tutorial: http://ambermd.org/
tutorials/advanced/tutorial7/index.htm
I noted that AMBER replica exchange requires that the parameters rgbmax =
999.0 and cut = 999.0. Why is this the case?
If I don't set the parameters as such, I get the following error:
*CUDA (GPU): Implementation does not support the use of a cutoff in GB
simulations. Require cut > 999.0d0.*
And then when I then run AMBER with this parameter inputted, I hit the
following issue:
ERROR: max cut must be < half smallest box dimension!
I know that my water box is too small. But to get a water box that does
abide by this cutoff, I'll need ~2000 x 2000 x 2000, which is drastically
larger than my current 113 x 113 x 113.
Has anyone else been through a similar situation (e.g. am I right in
generating a very large water box)?
Thanks for the help!
Jason
--
Jason Wang
Stanford University, Class of 2018
jwang198.stanford.edu
ᐧ
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Received on Fri Mar 02 2018 - 15:00:02 PST
