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

rasoul nasiri nasiri1355 at gmail.com
Mon Dec 21 20:20:34 CET 2009

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

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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091221/621b79d9/attachment.html>

More information about the gromacs.org_gmx-users mailing list