[gmx-users] Time for equilibration

XAvier Periole 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  
a good
idea. The time you need to run those simulations depends on the  
system. If
you see deviations you can try to run a bit longer. 100 ps is  
generally sufficient
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  
configuration that
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  
> topolgy.
> 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.
> Regards.
> --
> Sonali Dhindwal
> -- 
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