Bing Bing wrote:
Dear all,
I've tried to simulate a membrane system with POPC and protein following
Justin's tutorial. The system was minimized with 2 stages. First using
restraint on everything accept water for 10000 SD steps:-
Steepest Descents converged to Fmax < 1000 in 1785 steps
Potential Energy = -1.69457097061162e+06
Maximum force = 9.15408957613777e+02 on atom 24360
Norm of force = 7.53074616222725e+03
I've proceed with 2nd stage minimization without restraint,
Steepest Descents converged to Fmax < 1000 in 844 steps
Potential Energy = -1.87072963657420e+06
Maximum force = 9.14155621660386e+02 on atom 24360
Norm of force = 7.84646890755063e+03
The energy curve seems ok. With this, i went on with NVT equilibration (
restraint on protein) for 100ps. Both energy and temperature plot look fine
also.
But it failed while running NPT 1ns(restraint on protein also), it stop with
Range checking error, whereby the ci value exceeded the ci cutoff. it is
suggested that the minimzation might not done properly. But the minimization
were converged in both stages. Is there anything i missed out here?
That all looks fairly reasonable, but it seems you still need to be more
gentle. If the box density differs markedly from the expected value
(presumably about 1 g/mL for protein+membrane in water) then the NPT
transition will be sharp. You may need to choose a smaller integration
step size during the equilibration, or go back and choose a better box
size. Obviously, use nstxout=1 and watch where the breakage starts to
happen. That may clue you in to a problem.
Mark
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