I use Amber14. All the input files i used are attached here. min0.in and min1.in are the input files for minimization and md1.in for equileberation .
-----Original Messages-----
From: "Ñî´¨" <junaid.hust.edu.cn>
Sent Time: Monday, December 15, 2014
To: amber.ambermd.org
Cc:
Subject: Error in Box Dimension
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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- application/octet-stream attachment: min0.in
- application/octet-stream attachment: min1.in
- application/octet-stream attachment: heat.in
- application/octet-stream attachment: md1.in
Received on Mon Dec 15 2014 - 21:30:02 PST
