On Wed, Mar 30, 2016, Jinfeng Huang wrote:
>
> I have encounted a problem with sander.MPI procedure. I
> use ambertools 15 without amber 14, my operate
> system is Ubuntu 10.10,and I change the parameter of
> $AMBERHOME/AmberTools/src/sqm/qm2_dftb_module.F90” from 700 to 1500.
First, it's not clear what parameter was changed, or why. Are you running
a QM/MM simulation with the DFTB method?
> 1）If I conduct a MD simulation of structure A with sander.MPI, and the simulation stoped without any error messages.
> =======ended at this place===========
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------- -------------------------------------------------------
> | Local SIZE OF NONBOND LIST = 1360159
> | TOTAL SIZE OF NONBOND LIST = 16449139
> ===================================
Have you set nstlim=10 and ntpr=1? Does that give any additional information?
Are you sure you are capturing all of the error outputs (for example, if this
calculation is being run through a queueing system)? Does is make a
difference if you turn off QM/MM, or use a different Hamiltonian?
These are the sorts of debugging things that are likely to narrow down the
scope of the problem. Just saying that "the simulation stopped" does not
provide enough information for people on the mailing list to be able to help.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 30 2016 - 09:00:03 PDT
