Justin,<br><br>What temperature for NVT phase should be in<br><br>gen_temp = 323 <br><br>Does this parameere must be equal to the ref_t ?<br><br>I've obtain strange results after NVT with<br>ref_t = 297 297 297 <br>
<br>for protein in DMPC bilayer.<br><br>The bilayer with water parts diffused in up and down direction of the box relative protein<br>Why this should occur ? Might I alpy posres for lipid in NVT phase ?<br><br><div class="gmail_quote">
2011/11/11 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">
<br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Justin<br>
<br>
I'll try to do that things.<br>
<br>
Some addition questions<br>
<br>
1) About nvt and apt equilibration<br>
<br>
As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID.<br>
But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx )<br>
For my system composed of protein dmpc and water :<br>
<br>
ref_t = 323 297 323 ;<br>
<br>
Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition)<br>
ref_t = 297 297 297<br>
or each value must correspond to the temperature of phase transition of the individual element ?<br>
ref_t = 323 297 323 ;<br>
<br>
Does thic correct for both NPT and NVT ensembles ?<br>
<br>
</blockquote>
<br></div>
It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
James<br>
<br>
2011/11/11 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>>><div class="im"><br>
<br>
<br>
<br>
James Starlight wrote:<br>
<br>
Justin,<br>
<br>
Could you tell me what difference in inflategro parameters (<br>
cut-off for lipid removing and scaling factors) should I make<br>
for insertion protein in another bilayes in comparison tu tutorial ?<br>
<br>
<br>
I've never made any changes; it's always worked just fine.<br>
<br>
<br>
Now I'm working with DMPC. I've inserted symmetrical alpha<br>
helices protein in this bilayer but inflategro deleate 2 lipid<br>
from upper and just 1 from lower layer. It's strange because I<br>
suppose that equal bilayer molecules would be removed :o<br>
<br>
<br>
The number of lipids that are removed will depend on the starting<br>
configuration of the membrane and thus where lipids are relative to<br>
the protein. Theoretically, a symmetrical protein should delete an<br>
equal number of lipids from each leaflet, if the geometry of the top<br>
and bottom leaflets is comparable. Either try placing the protein<br>
at a different location to achieve equivalent removal or manually<br>
delete a lipid and be sure to equilibrate adequately.<br>
<br>
<br>
<br>
On Inflategro's sites I havenot found such specifity for above<br>
parameters for different bilayers :(<br>
<br>
<br>
The cutoffs specified are simple grid search parameters. They do<br>
not necessarily need to be altered depending upon the lipid type.<br>
<br>
<br>
-Justin<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>