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

[Justin A. Lemkul]

rasoul nasiri wrote:
> 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?
> 

I would be extremely suspicious of any results you get.  As you've been told 
before, secondary structure is a fixed aspect of a MARTINI CG simulation. 
Making changes is somewhat arbitrary and may lead to artifacts that you can't 
anticipate.  Besides, if you only know percentages of secondary structure (from 
CD I assume?) then you don't really know the structures and sequences that are 
changing, do you?

Net result: this particular CG model is probably not suitable for such a simulation.

-Justin

> Best regards
> Rasoul
> 
> On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

========================================