Hi,
I am conducting a thermodynamic integration (TI) calculation using pmemd
for a system containing a box of ionic liquid and rare earth elements. My
goal is to compute the free energy change associated with mutating one rare
earth element (RE1) into another (RE2). I have prepared the parameter and
restart files using parmed, and I am applying the softcore potential
exclusively to the rare earth atoms. However, when I attempt to run the
calculation, I encounter the following error:
''*Note: The following floating-point exceptions are signalling:
IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL*
*Note: The following floating-point exceptions are signalling:
IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMALERROR: 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.*''
Any help in this regard would be appreciated.
Thank you.
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Received on Wed Aug 28 2024 - 09:00:01 PDT
