[gmx-users] Time for equilibration

XAvier Periole x.periole at rug.nl
Thu Apr 15 11:45:22 CEST 2010


for the position restrain simulations have a llok at :
http://www.gromacs.org/Documentation/How-tos/Position_Restraints

Starting from an homology model you should expect some relaxation
of the structure during the simulation.

On Apr 15, 2010, at 11:06 AM, sonali dhindwal wrote:

> 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 good
> idea."
> 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  
> experimental
> conditions (T, pH) as well as the crystal contacts if X-ray were  
> used, dynamics
> of 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 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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