Justin,<br><br>Could you tell me if I want to simulate self-organization of the pure lipid bilayer starting from the initial random placed molecules in water. Does this simulation need in pre-md NVT and NPT equilibration? What the average time for NPT? I think that If this stage should occur it must be consist of long ( tens of NS ) preequilibration. <br>
<br><br><br>James<br><br><div class="gmail_quote">2011/10/21 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
You'll learn far more by discovering it yourself.<br>
</blockquote>
<br></div>
I stand by this statement. Perhaps some kind person with sufficient time on their hands will do your literature searching for you, but I do not, sorry. The information you need is out there. Start with the primary citation for whatever force field you want and search databases for citing articles or check out the references therein. Even Google can pull up very useful results within seconds, provided you've given sufficiently specific keywords.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
<br>
That's why at the present moment I'm examining different force fields and their implementation to the different systems. Could you recomend me some survey arcticle when I could find something usefull for this ? In particular I wounder to know about parametrisation for the membrane systems? Previosly I've found that charmm ff is ,ost accurasy in the case of such examination but I've not been able to rapametrise my bilayers via this ff yet ;x<br>
On other hand I have not difficulties with GROMOS ff for different systems ( e.g I've obtained very stabile systems durins some ns of simulations but I dont know about accuracy of the parametrisation of this ff in the case of membrane system for example .<br>
<br>
Finally I'm looking for tutorial for simulation of the pure lipids. E.g I want to simulate of different physical events on my membrane ( e.g I want to overkill my membrane by hyperpolarisation or other electrostatic effects emerged on the different steps of my simulation ) Could you also recomend me methodical literature for this styding?<br>
<br>
<br>
<br>
James<br>
<br>
<br></div>
-- ==============================<u></u>__==========<div class="im"><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><div class="im">
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__<a href="http://vt.edu/Pages/Personal/justin" target="_blank"><u></u>vt.edu/Pages/Personal/justin</a><br>
<<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a>><br>
<br>
==============================<u></u>__==========<br></div><div class="im">
-- 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>><br>
<a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__<u></u>mailman/listinfo/gmx-users</a><div class="im"><br>
<<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a>><br>
Please search the archive at<br></div>
<a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists/Search</a><div class="im"><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>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@<u></u>gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists</a><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a>><br>
<br>
<br>
</blockquote><div><div></div><div class="h5">
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<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/<u></u>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/<u></u>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/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>