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 <[email protected]> wrote:
From: XAvier Periole <[email protected]>
Subject: Re: [gmx-users] Time for equilibration
To: "Discussion list for GROMACS users" <[email protected]>
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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