[gmx-users] Time for equilibration

[sonali dhindwal]

Thanks for the answer,
My protein strucutre is a homology model,,on which i want to do the simulation. and the change in conformation after MD simulation is more than RMSD of 2 Angstrom, that too in  the active site of the protein
and you said that "Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a goodidea."
How we can do this ??
and you also mentioned that time period could b increased from 100 to 500 ps, does increase in time will be helpful in not distorting the strucutre ?
Regards
--
Sonali Dhindwal

--- On Thu, 15/4/10, XAvier Periole <x.periole at rug.nl> wrote:

From: XAvier Periole <x.periole at rug.nl>
Subject: Re: [gmx-users] Time for equilibration
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, 15 April, 2010, 1:46 PM


The distortion of a protein starting structure can result from various reasons:1- experimental determination of the structure: this include the experimentalconditions (T, pH) as well as the crystal contacts if X-ray were used, dynamicsof some part of the molecule if NMR.2- the manner you solvate and equilibrate. Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a goodidea. The time you need to run those simulations depends on the system. Ifyou see deviations you can try to run a bit longer. 100 ps is generally sufficientbut 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 thatare 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 fluctuationof 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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