<br><br>
<div class="gmail_quote">On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br> I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules.<br>
I am using CHARMM forcefield with Tip3p water.<br> The ffnonbonded.itp file of the forcefield has non-bonded parameters for tip3p water. Can I achieve the above by changing these parameters?<br> <br></blockquote><br></div>
That depends on your definition of "modify," but yes, in a way, you can make changes here. </blockquote>
<div> </div>
<div>1) Modify - Multiply sigma and epsilon by a constant<br></div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">If yes, will this also change the non-bonded parameters for water - water interaction?<br></blockquote></div>
</blockquote>
<div>2) Is there a way to add a new ifdef perhaps such that a modified sigma and epsilon can be used for water-protein interactions and the unmodified parameters can be used for water-water interactions?</div>
<div> </div>
<div>Pooja</div>
<div> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> <br></blockquote><br></div>Yes.<br><br>-Justin
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Pooja<br><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br><br></blockquote><br></div>-- <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><font color="#888888">-- <br>
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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>