<div dir="ltr">My system is a self-assembled cyclic peptide, I am trying to extract PMF to pull one of the terminal cyclic peptide. I have collected 25 windows starting from 0.5nm with 0.05nm window size. the histogram shows up to 0.7nm all the windows are overlapped around 0.5nm, and poor sampling from 0.6 to 0.75nm. from 0.75nm the sampling is perfect. each cyclic peptide has 8 residues and the terminal one forms 8 hbonds with the 2nd cyclic peptide. I guess due to this strong hbonding, the sampling window up to 0.7nm is very poor. If we extend the simulation only for these windows can we get proper sampling windows? this observation is from last 10ns of 20ns simulation. <br>
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Message: 3<br>
Date: Mon, 07 Nov 2011 10:20:07 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EB7F727.3000504@vt.edu">4EB7F727.3000504@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Vijayaraj wrote:<br>
> and also I tried to plot the PMF curve from this data, I got few warning<br>
> messages like "no data point in bin 20, You may not get a reasonable<br>
> profile. Check your histograms!". the histogram shows poor sampling from<br>
> 0.6 nm to 0.7 nm, and the windows in this position completely overlaps<br>
> at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm<br>
> window to get the restrain distance converged?<br>
><br>
<br>
It is still somewhat difficult to provide any useful advice. You haven't stated<br>
what your system is, how your windows were assembled, at what interval they<br>
exist, or how many you have. The above warnings suggest that you've either set<br>
up the windows wrong, have insufficient data, or are analyzing parts of the<br>
trajectory you shouldn't be (i.e. initial times that are equilibration).<br>
<br>
-Justin<br>
<br>
> On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj <<a href="mailto:vijayaraj81@gmail.com">vijayaraj81@gmail.com</a><br>
> <mailto:<a href="mailto:vijayaraj81@gmail.com">vijayaraj81@gmail.com</a>>> wrote:<br>
><br>
> Hello,<br>
><br>
> Thanks for the suggestions. I did umbrella simulation for 20ns and<br>
> the pull force is as below.<br>
><br>
><br>
> 19960.0000 -6.78192<br>
> 19962.0000 33.3579<br>
> 19964.0000 -3.1808<br>
> 19966.0000 -15.0304<br>
> 19968.0000 -55.4436<br>
> 19970.0000 -38.9422<br>
> 19972.0000 -9.41927<br>
> 19974.0000 -5.95981<br>
> 19976.0000 0.626319<br>
> 19978.0000 2.28736<br>
> 19980.0000 23.5115<br>
> 19982.0000 10.6415<br>
> 19984.0000 -0.233446<br>
> 19986.0000 8.26525<br>
> 19988.0000 36.7656<br>
> 19990.0000 26.6017<br>
> 19992.0000 64.43<br>
> 19994.0000 53.3844<br>
> 19996.0000 18.3834<br>
> 19998.0000 39.8988<br>
> 20000.0000 43.6291<br>
><br>
> I expect the force should be converged. my understanding might be<br>
> wrong. I have poor knowledge about this umbrella sampling<br>
> convergence and image selection for the PMF calculation. is this<br>
> fluctuation in force due to pulling group motion out of box? can you<br>
> give me some idea about the selection of images for PMF calculation?<br>
> I found from the pullx files that the COM distance converges after<br>
> few ns of simulation. I understood that we cant do PMF study with<br>
> pull=constraint.<br>
><br>
> Vijay.<br>
><br>
><br>
> Message: 2<br>
> Date: Mon, 07 Nov 2011 09:07:21 -0500<br>
> From: <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> <mailto:<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>><br>
> Subject: [gmx-users] umbrella sampling with "pull=constraint"<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:20111107090721.jy8zfzhvh4ccw0ws@webmail.utoronto.ca">20111107090721.jy8zfzhvh4ccw0ws@webmail.utoronto.ca</a><br>
> <mailto:<a href="mailto:20111107090721.jy8zfzhvh4ccw0ws@webmail.utoronto.ca">20111107090721.jy8zfzhvh4ccw0ws@webmail.utoronto.ca</a>>><br>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
> format="flowed"<br>
><br>
> Dear Vijay:<br>
><br>
> Can you please provide evidence for your claim that the harmonic<br>
> potential is not applied properly, since you may decide to use<br>
> pull=umbrella once you have set that up correctly. Importantly,<br>
> movement out of the unit-cell is not a problem, as discussed a<br>
> lot on<br>
> this list. Nevertheless, you do need to worry about which images are<br>
> used to derive the pulling forces. You can often do that by a<br>
> judicious selection of pull_pbcatom (read about that on-list and in<br>
> the manual). In some cases, however, pull_pbcatom can not assist<br>
> enough and you are forced to make the box larger. None of this is<br>
> alleviated by pull=constraint, which is why I'm not going to answer<br>
> your question about your .mdp parameters at this point. Let's<br>
> get the<br>
> problems identified and solved first with pull=umbrella.<br>
><br>
> Chris.<br>
><br>
><br>
> -- original message --<br>
><br>
> Hello,<br>
><br>
> I have done umbrella sampling with "pull=umbrella" and I found<br>
> that the<br>
> pulling group has high fluctuations and sometimes moving out of the<br>
> periodic box. I think that the harmonic potential is not<br>
> properly applied<br>
> and thus the pulling group is not retained with the specified<br>
> COM distance<br>
> between the reference and pulling group. Can we use<br>
> pull=constraint option<br>
> to retain the pulling group within the COM distance? my pulling<br>
> code is as<br>
> bellow with restrain at 0.5nm distance from ref group. I just<br>
> want to get<br>
> some idea about this pull code modification.<br>
><br>
> pull = constraint<br>
> pull_geometry = distance<br>
> pull_dim = N N Y<br>
> pull_start = no<br>
> pull_ngroups = 1<br>
> pull_group0 = Chain_A<br>
> pull_group1 = Chain_B<br>
> pull_init1 = 0.50<br>
> pull_rate1 = 0.0<br>
> pull_k1 = 1000<br>
> pull_nstxout = 500<br>
> pull_nstfout = 500<br>
><br>
><br>
> Regards,<br>
> Vijay.<br>
><br>
><br>
><br>
> -<br>
><br>
><br>
><br>
><br>
><br>
<br>
--<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>
========================================<br></blockquote></div><br></div>