I would use grep and cut to take the atom numbers of the residues I want to restrain and direct them into an index file with [res_sol] at the top. Then use genrestr to generate restraints for these atoms using the -n option. Then conditionally include this restraint file (.itp file) in my topology when you use -DPOSRES_res_sol (or whatever just make it match what's in the top file) in your mdp file.<br>
<br>Thats how I would put position restraints on parts of my system. I think different constraints are answered here too :)<br>Good luck,<br>Oliver<br><br><br><br><div class="gmail_quote">On 2 December 2010 08:21, David Rodríguez <span dir="ltr"><<a href="mailto:david.rguez.diaz@gmail.com">david.rguez.diaz@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;"><div class="gmail_quote">2010/12/2 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><div class="im">
<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>On 2/12/2010 12:51 PM, Guido Polles wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
I know it looks a little bit strange, but i was trying to restrain<br>
just some water in my system.<br>
Now, if i put something like<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
I put restraints on all the molecules.<br>
</blockquote>
<br></div>
Yes, that directive will pertain to all the molecules that have that [ moleculetype ]. I'm not sure if you only want position restraints on some of your water molecules.<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I thought about a turnaround, just making a second water molecule<br>
type, but now complains about using more than one settle type.<br>
Is there any other way to do it?<br></blockquote></div></blockquote></div><div><br>Guido, <br></div><div>You may find this thread useful:<br><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html</a><br>
</div><div class="im"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
And if I follow the "Suggestion: change the least use settle<br>
constraints into 3 normal constraints" I have to worry about some kind<br>
of huge loss in performance?<br>
</blockquote>
<br></div>
I would expect the non-settle waters to use the solvent-optimized loops in the normal way, so there should be no difference in execution time between the unrestrained all-settle simulation and the partly-restrained party-settled simulation. Obviously, this is straightforward to test.<br>
<font color="#888888">
<br>
Mark</font><div><div></div><div><br>
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</div></div></blockquote></div></div><font color="#888888"><br><br clear="all"><br>-- <br>David Rodríguez Díaz, PhD Student<br>Fundación Pública Galega de Medicina Xenómica (SERGAS)<br>Web page: <a href="http://webspersoais.usc.es/persoais/david.rodriguez.diaz" target="_blank">http://webspersoais.usc.es/persoais/david.rodriguez.diaz</a><br>
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