<div dir="ltr">Thanks for you prompt reply - I'll try that and post back.<br>-SA<br><br><div class="gmail_quote">On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;"><div class="im"><br>
<br>
Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis).<br>
Problem is, that with every pull settings I have tried the ligand gets "stuck" on the protein's center of mass. How can I make it go all the was to the bulk water?<br>
It always gets stuck on the COM. And I've tried using both umbrella and constant force, so I'm getting the feeling that I'm missing something trivial.<br>
<br>
Here's an example of one set of pull-parameters I tried:<br>
-------------------------------><br>
pull = constant_force<br>
pull_geometry = distance<br>
</blockquote>
<br></div>
You can only use the distance method if the distance between pull_group0 and pull_group1 is constantly decreasing or increasing. If you're moving through a channel, you should use the position method in conjunction with an appropriate pull_vec1.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
pull_dim = N N Y<br>
pull_start = yes ; define initial COM distance > 0<br>
<br>
pull_ngroups = 1<br>
pull_group0 = Protein<br>
</blockquote>
<br></div>
You probably need a better reference group, i.e. some subset of residues that forms the entrance or exit from the channel, but you may be able to get away with this reference group if you using a more appropriate pull_geometry, as suggested above.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
pull_group1 = Ligand<br>
;pull_rate1 = -0.001 ; 0.01 nm per ps = 10 nm per ns<br>
pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>
<------------------------------<br>
<br>
Can anyone help enlighten me as to what I am doing wrong?<br>
Thanks,<br>
-Shay<br>
<br>
P.S.<br>
Using gromacs 4.0.7.<br>
<br>
</blockquote>
<br></div>
-- <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> | (540) 231-9080<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>
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