<div>Hi Justin,</div>
<div>Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did something wrong? Is it always the same order for different systems? Can you please give me some advice about it?? Many Thanks in Advance/ Jamie<br>
<br></div>
<div class="gmail_quote">On Sat, Aug 15, 2009 at 6:37 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br>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></blockquote><br></div>If your topology has the appropriate #ifdef POSRES, and you have "define = -DPOSRES" in your .mdp file, then it worked :) Position restraints are applied during mdrun, and show up in the .log file as "Position Rest." entries.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br> Jamie Seyed wrote:<br><br> Hi Mark,<br> Thanks for the answers. One question still remains for me: in<br> the fws<br> tutorial for PR step it only uses the pr.mdp (define = -DPOSRES)<br> and run<br>
grompp followed by mdrun... Am I missing some thing? Because I<br> can not see<br> it introduces something that to be restrained..?? Would you<br> please let me<br> know what I am missing here?? Many Thanks in Advance/Jamie<br>
<br><br> pdb2gmx automatically produces a posre.itp file, whose position<br> restraint contents are #included from the .top file it produces, and<br> whose function is sensitive to the -DPOSRES option. Search the wiki<br>
for discussion of this machinery.<br><br> Mark<br><br> On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham<br></div> <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>wrote:
<div>
<div></div>
<div class="h5"><br><br> Jamie Seyed wrote:<br><br> Dear all,<br> I have questions regarding the position restrain md. I<br> tried to find the<br> answer of my questions from the mailing list, but it is<br>
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<br>
for this case we<br> can<br> simply write "system" because system is made by protein<br> and non-protein??<br><br> It includes the whole system, but it is often a good idea<br>
not to couple<br> groups of heterogeneous heat capacity to the same<br> 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<br> restrain and which<br><br> one not, because it included all??<br><br> Temperature coupling has no linkage with position<br>
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<br>
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<br> that need to be<br><br> constrained, in the generated index file I will get<br> system and all its<br> parts<br>
and an extra part for my specific part that need to be<br> constrain...Is that<br> ok??<br><br> "constraints" are different from "restraints" in GROMACS<br>
usage. make_ndx<br> does allow you to generate new index groups, but you will<br> need to (re-)read<br> the relevant manual sections to understand that neither of<br> 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<br> position<br><br> restrain md should I use "tc_grps=MOL SOL" (according<br>
to fws tutorial)<br> or<br> I need only write "tc_grps=MOL"?? Many Thanks in<br> Advance/Jamie<br><br> 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<br> strategic<br> objective. Hopefully some of the links will move you towards<br>
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>
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<br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<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>
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