<div>Hi, </div>
<div>How can I make sure that position restraint is actually applied (after grompp & mdrun)? When I grep "POSRES" or "posres" I can not see any information... Many Thanks in Advance/Jamie<br><br></div>
<div class="gmail_quote">On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="im">Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Mark,<br>Thanks for the answers. One question still remains for me: in the fws<br>tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run<br>
grompp followed by mdrun... Am I missing some thing? Because I can not see<br>it introduces something that to be restrained..?? Would you please let me<br>know what I am missing here?? Many Thanks in Advance/Jamie<br></blockquote>
<br></div>pdb2gmx automatically produces a posre.itp file, whose position restraint contents are #included from the .top file it produces, and whose function is sensitive to the -DPOSRES option. Search the wiki for discussion of this machinery.<br>
<font color="#888888"><br>Mark<br><br></font>
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<div class="h5">On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Jamie Seyed wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all,<br>I have questions regarding the position restrain md. I tried to find the<br>answer of my questions from the mailing list, but it is not clear yet.<br>
In the fws tutorial when it says (in the pr.mdp)<br>tc_grps=Protein non-protein<br>(1) Doesn't that mean everything in the system? I think for this case we<br>can<br>simply write "system" because system is made by protein and non-protein??<br>
<br></blockquote>It includes the whole system, but it is often a good idea not to couple<br>groups of heterogeneous heat capacity to the same thermostat. That said, if<br>the groups are too small, you get other problems. See also<br>
<a href="http://oldwiki.gromacs.org/index.php/temperature_coupling" target="_blank">http://oldwiki.gromacs.org/index.php/temperature_coupling</a><br><br>(2) In this case how program recognize which one should restrain and which<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">one not, because it included all??<br><br></blockquote>Temperature coupling has no linkage with position restraints. You defined<br>
the latter in your .top file.<br><br>(3) This step is required for every system or only proteins??<br>It may or may not be useful in achieving stable equilibration for any<br>system. See<br><a href="http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation" target="_blank">http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation</a><br>
<br>(4) If I want to make an index file and I specify a group that need to be<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">constrained, in the generated index file I will get system and all its<br>parts<br>and an extra part for my specific part that need to be constrain...Is that<br>
ok??<br><br></blockquote>"constraints" are different from "restraints" in GROMACS usage. make_ndx<br>does allow you to generate new index groups, but you will need to (re-)read<br>the relevant manual sections to understand that neither of these algorithms<br>
uses index groups. (Or to prove my memory wrong!)<br><br>(5) In my case I have a molecule (MOL) and water (SOL), for position<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">restrain md should I use "tc_grps=MOL SOL" (according to fws tutorial)<br>or<br>I need only write "tc_grps=MOL"?? Many Thanks in Advance/Jamie<br>
<br></blockquote>The latter won't work, for all atoms must be members of a<br>temperature-coupling group if any are.<br><br>What you actually need is a clear understanding of your strategic<br>objective. Hopefully some of the links will move you towards that.<br>
<br>Mark<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/mailman/listinfo/gmx-users</a><br>
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