[gmx-users] Time for equilibration
x.periole at rug.nl
Thu Apr 15 10:16:52 CEST 2010
The distortion of a protein starting structure can result from various
1- experimental determination of the structure: this include the
conditions (T, pH) as well as the crystal contacts if X-ray were used,
of some part of the molecule if NMR.
2- the manner you solvate and equilibrate. Using position restrain on
heavy atoms of the protein first, and then on the Calphas is generally
idea. The time you need to run those simulations depends on the
you see deviations you can try to run a bit longer. 100 ps is
but can be extended to 500 ps, this is no problem.
3- the force field you are using might also trigger some "small"
deviations of the
protein. The protein structure might contain "strange" local
are not sable in the FF.
4- you set up, meaning time step, temperature, pressure, ...
Note finally that a deviation from the starting structure might just
be a fluctuation
of a labile region of the protein ...
On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote:
> Hello All,
> I have a protein of 576 amino acid long, and has a barell shape
> I have done MD simulation on it for 1ns, and my protein has got
> distorted shape, i.e, one of the strand became coil and other
> strands became small.
> I wrote this query before also, can it be possible that this is due
> to equilibration conditons i am giving, i am equilibrating it for
> 100 ps under NVT using brendenson coupling.
> What should be ideal time for equibrating the protein with solvent ?
> How should it be determined, or it is based on experimenting with
> different conditions ?
> Please help.
> Sonali Dhindwal
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