Hi,
Without more detailed information it's difficult to help. The
statement "I checked it on CPU" has practically no information
content. At the very least let us know what version of Amber you are
using as well as what your input file looks like, and ideally the
output leading up to the error message.
-Dan
On Sun, Dec 14, 2014 at 9:13 PM, 杨川 <junaid.hust.edu.cn> wrote:
> Dear Amber Users
> I am trying to simulate a protein with drug. First i use minimize the Protein and drug only. Then i minimize the whole system( Protein+drug+water box). After this i heated the Protein from 0K to 300K. Then i want to equilabrate the complex but it gives me the Following error. I checked it on CPU but it gives the same error. kindly give me some comments.
> Thank you
> "ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your system
> is a long way from an equilibrated density.
>
> Alternatively you can run with the CPU code until the density has converged
> and then switch back to the GPU code"
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Dec 14 2014 - 20:30:03 PST
