[gmx-users] How can I reconstruct the system in CGMD simulation?
Justin A. Lemkul
jalemkul at vt.edu
Mon Dec 21 20:51:36 CET 2009
rasoul nasiri wrote:
> 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?
>
There are several CG models out there, but I don't know much about them. The
nice thing about Gromacs is that it can use any force field you can find.
As for Go-models, you've already been given advice on that topic:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047496.html
-Justin
> Kind regards
> Rasoul
>
>
> On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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> <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 <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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