[AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box?

From: Jason Ku Wang <jwang198.stanford.edu>
Date: Fri, 2 Mar 2018 14:42:31 -0800

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/

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 Wang
Stanford University, Class of 2018
AMBER mailing list
Received on Fri Mar 02 2018 - 15:00:02 PST
Custom Search