On Tue, Jul 23, 2019, CROUZY Serge 119222 wrote:
>
>I'm facing a problem in a simulation of a protein in water (TIP3P) with
>counter ions and parallelepipedic periodic boundary conditions with
>polarization
>Here for only 800 ps
>Lines of output
>
>NSTEP = 500 TIME(PS) = 200.500 TEMP(K) = 299.31 PRESS = 74.5
> Etot = -74898.0013 EKtot = 9195.2868 EPtot = -84093.2881
> BOND = 209.7914 ANGLE = 541.8550 DIHED = 791.7732
> 1-4 NB = 278.1858 1-4 EEL = 3222.7867 VDWAALS = 38592.0323
> EELEC = -93496.7202 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 4227.8054 VIRIAL = 4014.3598 VOLUME = 132608.2186
> EPOLZ = -34232.9923
> Dipole convergence: rms = 0.849E-02 temperature = 0.64
> Density = 1.1683
You density seems way to high for a protein in water. What was the
initial density? How much water did you add at the tleap stage?
Have you visualized the simulation to look for odd behavior. It would
be a good idea to use the "checkstructure" action in cpptraj on a system
with this high a density to see if that flags any problems.
You might try setting barostat=2, or running with a non-polarizable
potential to see if any problems occur there. You should be aware that
(as far as I know) a *very* small fraction of Amber protein simulations
use polarizable potentials, so it's possible that there may be some
instabilities that people are not used to seeing.
...good luck...dac
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Received on Tue Jul 23 2019 - 15:30:03 PDT
