[gmx-users] How can I reconstruct the system in CGMD simulation?
Justin A. Lemkul
jalemkul at vt.edu
Mon Dec 21 20:23:32 CET 2009
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.
> Best regards
> 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/%7Emarrink/MARTINI/Coordinates.html> and
> another is water-1bar-303k.gro in :
> <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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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