[gmx-users] How can I reconstruct the system in CGMD simulation?

[rasoul nasiri]

Dear Justin,
Thank you for your message.

I have found some experimental evidence to suggest that the secondary
structure information of protein how change during the reaction of the
unfolding. In the other hand, I have percentage of the secondary structure
information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at
different time of reaction.
Could I perform CGMD simulation with MArtini force field for finding the
denaturation mechanism of the protein properly?

Best regards
Rasoul

On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> rasoul nasiri wrote:
>
>> Dear Cesar,
>> Thank you for your reply,
>>
>> There are two different kind of water gro in this site (one of them is
>> water.gro in :
>> http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html<http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html>and another is water-1bar-303k.gro in :
>>  http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html<http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html>. Is there difference between them?
>>
>
> Maybe, but if you do sufficient equilibration, it probably won't matter.
>
>
>  Can I build water.gro with coarse graining beads (P4) from spc216.gro with
>> using atom2cg.awk script?
>>
>>
> No.  This has been stated before - the awk script is explicitly for
> protein. And besides, each "W" CG particle corresponds to about four water
> molecules, so there is no trivial way to decide how to build the CG water
> system from spc216.gro.
>
>
>  Another question; How can I change secondary structure information during
>> CGMD simulation, If I want to perform CGMD simulation for finding of the
>> folding/unfolding mechanism in proteins completely? Because Martini CGFF
>> consider fix it.
>>
>>
> You specify the secondary structure when building the initial topology.  As
> you've been advised already, this "fixed" representation of secondary
> structure is going to be a major limitation of using the MARTINI force field
> for your simulations.  How do you know that whatever alternate secondary
> structure you've applied is valid?  If you have some experimental evidence
> to suggest that certain peptide regions convert between one form and
> another, that's fine, but how do you know that the pathway taken is not an
> artifact of your choice to abruptly impose a change in the topology?
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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