[AMBER] Simulation run issue

From: Sayan Poddar <phd1801271004.iiti.ac.in>
Date: Mon, 18 Nov 2019 11:33:03 +0530

Dear All,

I am trying to simulate glycans consist of four monosaccharides on Amber18.
I have tried it with two different buffer size of 10 and 12. But every time
the process gets halted with this error message.

*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.*

I have never faced this issue before. However this problem is being shown
by only two glycans. My other glycans run perfectly on Amber18.

Strangely those glycans which are not being able to simulate on Amber18
runs perfectly on Amber16 with exactly the same parameters as used in


*with regards*
*Sayan Poddar*
*Research Fellow*
*Discipline of Biosciences and Biomedical Engineering*
*Indian Institute of Technology Indore*
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Received on Sun Nov 17 2019 - 22:30:02 PST
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