<div dir="ltr">As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them.<br><br>Dariush<br><br><div class="gmail_quote">
On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha <span dir="ltr"><<a href="mailto:przemekbartha@gmail.com" target="_blank">przemekbartha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hello,<br>According to Justin's tutorial on umbrella sampling, <br>link: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html</a><br>
could anyone explain, if the molecules are restrained in any way in the umbrella sampling part?<br>What I mean, is when we pull molecule A from molecule B, we restrain "B" to that it does not follow "A" (by adding "pos_res" section in .itp file).<br>
In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I have got two .itp files for both molecules. Restraining LYS worked well for generating configurations, but failed for umbrella sampling.<br>My molecules (including LYS which was restrained) were "flying" randomly all over the box which resulted in incorrect PMF courve.<br>
<br>So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why?<br><br>thanks in advance,<br>Przemek<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<br>
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></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Kind Regards,<br>
Dariush Mohammadyani<br>Department of Structural
Biology<br>University of Pittsburgh School of Medicine<br>Biomedical Science
Tower 3<br>3501 Fifth Avenue<br>Pittsburgh, PA 15261<br>USA</div></div><br>
</div>