Dear Justin,<br>Thank you for your message.<br><br>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.<br>Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly?<br>
<br>Best regards<br>Rasoul<br><br><div class="gmail_quote">On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br>
<br>
rasoul nasiri wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Cesar,<br>
Thank you for your reply,<br>
<br>
There are two different kind of water gro in this site (one of them is water.gro in :<br>
<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html" target="_blank">http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html</a> and another is water-1bar-303k.gro in :<br>
<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html" target="_blank">http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html</a> . Is there difference between them?<br>
</blockquote>
<br></div>
Maybe, but if you do sufficient equilibration, it probably won't matter.<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script?<br>
<br>
</blockquote>
<br></div>
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.<div>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
<br>
</blockquote>
<br></div>
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?<div>
<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>