<div>Hi</div>
<div> </div>
<div>This is regarding the pull code.. I have followed your tutorial to get the PMF for distance between 2 atoms using the pull code. I want to know if one can bring the atoms closer rather than pull them apart? I want to start from the maximum distance and then bring them closer to check reversibility. Also, I dont think I can apply it a fixed vector (as in specify the vector from one atom to the other) because I dont think the path will be a straight line.</div>
<div> </div>
<div>Pooja<br><br></div>
<div class="gmail_quote">On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>Sai Pooja wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">The pull tutorial uses npt simulations.. is that required by the algorithm or can one use nvt after the system has been sufficiently equilibrated using npt?<br>
<br></blockquote><br></div>Use whatever conditions are appropriate for your system. Tutorials should not be viewed as the only applicable conditions, merely one such example of what might be done.<br><br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br> pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to<br> create a merged [moleculetype] to apply distance restraints. If<br> you're just trying to use a harmonic potential to define some<br>
sampling distance (for US), then distance restraints are not<br> necessary, just apply the pull code.<br><br> -Justin<br><br> Sai Pooja wrote:<br><br> Also, the chains do not diffuse apart in time since they are<br>
position restrained(some parts of each chain are ...)<br><br> On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a><br></div> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>
<div class="im"><br> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>>> wrote:<br><br> Hi,<br> I have 5 chains in my Protein. I want to apply distance<br>
restraints<br> for doing Umbrella Sampling for 2 atoms on different chains. Is<br> there a way to do this since the two chains have separater<br> itp files.<br> Pooja<br><br> -- Quaerendo Invenietis-Seek and you shall discover.<br>
<br><br><br><br> -- Quaerendo Invenietis-Seek and you shall discover.<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></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><br>
<tel:%28540%29%20231-9080>
<div class="im"><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>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
<div class="im"><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<br> <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<br> interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.
<div class="im"><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><br><br><br><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div></blockquote>
<div>
<div></div>
<div class="h5"><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> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><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>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></div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>