On Wed, Sep 10, 2014, Ibrahim Said wrote:
> My problem is The RMSD during equilibration phase increases approx.
> linearly, which may indicate unfolding of the protein . I ran equilibration
> for 1 ns. Please, any one has sugestions.
> Keep solute fixed with weak restraint
> 500.0
Actually, the correct comment would be: keep solute fixed with very large
constraint. Consider using a value 2 orders of magnitude smaller. However,
this is unlikely to be the cause of waht you see.
> RES 1 181
> END
> END
>
> The protocol for equilibration is
> &cntrl
> imin = 0, irest = 1,
> ntb = 2, ntx = 5,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> temp0 = 298.0,
> ntt = 3, gamma_ln = 1.0, ntp = 1,
> nstlim = 100000, dt = 0.002,
> ntpr = 500, ntwr = 500,
> ntwx = 500,
> &END
Here here are no constraints, so the peptide is free to do whatever it wants.
Are you sure that its RMS to the starting structure is supposed to stay small?
...dac
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Received on Thu Sep 11 2014 - 05:30:02 PDT
