Hi Vitaly,
thank you for the suggestions. the energy plots seemed fine. I switched to the serial code for 25ps, npt equilibration ran successfully.
Then I switched back to the parallel sander.MPI. The simulations has been running for about 10 ns without failing so far.
With best regards, Maria.
On Jul 30, 2012, at 5:53 PM, Dr. Vitaly V. G. Chaban wrote:
>>> 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 Thu Aug 02 2012 - 12:30:04 PDT
