On Mon, Jul 30, 2012 at 3:32 PM, Maria Minakova
<mariabiophysics.gmail.com> wrote:
> Hi everyone,
>
> 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
>
> ------------------------------------------------------------
>
> Exited with exit code 1.
>
> Resource usage summary:
>
> CPU time : 15057.00 sec.
> Max Processes : 183
> Max Threads : 571
>
> The output (if any) follows:ASSERTion 'e' failed in nonbond_list.F90 at line 849.
>
> ...
>
> "
>
> Input file and output (no restraints, small time step version) are attached.
>
--
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
