[gmx-users] NPT equilibration failing at high temperature

Justin Lemkul jalemkul at vt.edu
Mon Mar 12 15:42:26 CET 2018

On 3/12/18 3:42 AM, Joe Jordan wrote:
> You should use the hint in the error message, that the system is not well
> equilibrated. Try a shorter time step or a double precision minimization.
> Also see
> http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
> for info.

A shorter time step is probably the best solution. Such high 
temperatures lead to extremely frequent, high-energy collisions between 
water and solute (and everything, really) leading to high forces. Most 
force fields haven't been validated for use at such temperatures, 
because you're well beyond boiling the water at that point.


> On Mon, Mar 12, 2018 at 7:18 AM, brataraj ghosh <bratarajghosh at gmail.com>
> wrote:
>> Hi
>> I am trying to simulate a system contains two identical protein chains.
>> I am equilibrating the system at 7 different temperatures. All the nvt ones
>> have completed without any errors. 5 npt ones are also completed but in
>> case of two highest temperatures 679.35 k and 800.0 k it is showing this
>> following error
>> "2 particles communicated to PME rank 2 are more than 2/3 times the cut-off
>> out of the domain decomposition cell of their charge group in dimension x.
>> This usually means that your system is not well equilibrated."
>> Any suggestions how to solve this issue?
>> --
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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