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).
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.
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Received on Mon Jul 30 2012 - 13:00:04 PDT
