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>
<div class="gmail_quote">On Fri, Apr 1, 2011 at 7:32 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"><br>pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a merged [moleculetype] to apply distance restraints. If you're just trying to use a harmonic potential to define some sampling distance (for US), then distance restraints are not necessary, just apply the pull code.<br>
<br>-Justin<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">
<div class="im">Also, the chains do not diffuse apart in time since they are position restrained(some parts of each chain are ...)<br><br></div>
<div class="im">On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <<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>>> wrote:<br>
<br> Hi,<br> I have 5 chains in my Protein. I want to apply distance 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 itp files.<br>
Pooja<br><br> -- Quaerendo Invenietis-Seek and you shall discover.<br><br><br><br><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br><br></div></blockquote><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><font color="#888888">-- <br>
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