Dear Chris,<div><br></div><div>Thank you for the code. I did check out pull_pbcatomN, and thank you for the heads up that it is a global index. I used a central atom in the box for each of the two groups as pull_pbcatom. </div>
<div><br></div><div>After using the code below with a rate constant of ~ 5500 for about 100 ps, I realized that the atoms in different leaflets were being pulled in the same direction. I wanted certain atoms of either leaflet to be restrained to the bilayer center. However, the code pulls all the atoms in the same direction, such that atoms from one leaflet do approach the bilayer center, but those from the other leaflet tend to get further away from the bilayer center. Thus, one actually needs two groups to be pulled, one each for the atoms in each leaflet. Once this was fixed, the code worked just fine.<br>
<br>Again, thank you. <br><br></div>
<div>Maria<br></div><div><br></div><div><br><br><div class="gmail_quote">On Tue, Sep 7, 2010 at 3:40 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</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;">
Maria, try this. There actually is a lot of this on the mailing list, so I suggest checking it a little deeper for your next querry, or at least outlining how you looked and what you found so that it is clear you have tried.<br>
<br>
Also, read about pull_pbcatomN and think carefully about how you want to set that up. It is a *global* index.<br>
<br>
; COM PULLING<br>
pull = umbrella<br>
pull_geometry = position<br>
pull_dim = N N Y<br>
pull_start = no<br>
pull_nstxout = 500<br>
pull_nstfout = 500<br>
pull_ngroups = 1<br>
pull_group0 = <<<bilayer-group>>><br>
pull_pbcatom0 = 0<br>
pull_group1 = <<<pulled-group>>><br>
pull_pbcatom1 = 0<br>
pull_init1 = 0 0 0.0<br>
pull_rate1 = 0<br>
pull_k1 = <<<force-constant>>><br>
pull_vec1 = 0 0 0<br>
<br>
-- original message --<br>
<br>
<br>
The manual does discuss restraining to a plane, but this must be the plane<br>
in which the atom is already present.<br>
<br>
[ position_restraints ]<br>
; ai funct fc<br>
...<br>
3 1 1000 0 0<br>
<br>
How about restraining the atom to some other plane? For example, how about<br>
restraining a phosphate group initially at the lipid-water interface to the<br>
bilayer center (for whatever fancy reasons) ? Won't this require pulling the<br>
atom to that plane first?<br>
<br>
If it can be achieved using the position restraints alone, it is not clear<br>
to me how to do this?<br>
<br>
-Maria<br>
<br>
<br>
<br>
On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul <jalemkul at <a href="http://vt.edu" target="_blank">vt.edu</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
maria goranovic wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I want to restrain certain atoms of my simulation to the plane<br>
perpendicular to the bilayer normal, and at the bilayer center. Can someone<br>
please provide a quick guide on how to do this? I read the pull-code<br>
options, but restraining to a plane did not seem possible?<br>
<br>
<br>
</blockquote>
You can restrain atoms to a plane using position restraints. See the<br>
manual for an example.<br>
<br>
-Justin<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
--<br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
<br>
</blockquote></blockquote>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
</div>