>> My equilibration of the synthetic+chromophore systems fails consistently after switching to NPT from NVT at 300 K.
>> The system was minimized, heated to 300 K and equilibrated (nvt) with harmonic restriction to the helix, so I get not unfolding artifacts before the production runs.
>> When I switch to Langevin dynamics, the simulation always fails after first ~30 ps (6 attempts with varying conditions: smaller time step, strong/weak/no harmonic restrictions for the macromolecule).
>>
>
>
> Hmm... Did it always fail after ~30ps regardless the time-step? What
> the time-step are you using normally for this system?
>
> What about the energy vs time plot? This is your first debugging stage.
>
>
>
>
>> When I look at the trajectory and restarts in VMD, i don't see any significant disturbance to the molecule structure or collapsed atoms.
>> The output energies are not very different from the beginning snapshot, no signs of sudden change in box size, density, or vdw energies.
>>
>> Could you suggest some debugging strategies?
>>
>>
>> Thank you, Maria Minakova.
>>
>> Additional info:
>> the out.* has this error information:
>> "
>> ...
>>
>> mpirun sander.MPI -O -o output_polypr_equil_7.out -i equil_300K_npt_norestr.in -
>> p 0a_watsalt_hovdw.prmtop -c polypr_min_6.rst -r polypr_min_7.rst -x polypr_equi
>> l_7.mdcrd
I would also try serial executable. In certain [unpredictable] cases,
parallel code crashes while the serial one works fine.
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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Received on Mon Jul 30 2012 - 15:00:03 PDT
