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

[rasoul nasiri]

Hi,
Thank you for your quick reply.

Is there another CGFF for this purpose that Gromacs can read it? What is
your opinion about CG GO model?

Kind regards
Rasoul


On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>>        <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>
>>        <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
>
> ========================================
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