I'm a bit confused about your inputs. here are some suggestions:
first, don't do REMD until you've already done normal MD on your system.
You need to equilibrate it anyway, so that will let you see what is an
error related to REMD compared to normal MD.
second, you mention GB but you say you have a "water box". these are
probably not both correct. Are you using implicit solvent (GB), with no
periodic box, or explicit solvent and periodic box, with igb=0? clearing
that up will probably solve at least this initial problem you described
below.
third, if you do REMD in explicit water, keep in mind that you'll need to
equilibrate the box volume first, then do REMD in NVT (NPT isn't supported
in Amber. Also, when considering your box, keep in mind any conformational
changes that might happen at elevated temperature. Will the box still
enclose the solute at high T?
On Fri, Mar 2, 2018 at 5:42 PM, Jason Ku Wang <jwang198.stanford.edu> wrote:
> 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 - 15:00:04 PST
