and also I tried to plot the PMF curve from this data, I got few warning messages like "no data point in bin 20, You may not get a reasonable profile. Check your histograms!". the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window to get the restrain distance converged?
On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj <vijayara...@gmail.com> wrote: > Hello, > > Thanks for the suggestions. I did umbrella simulation for 20ns and the > pull force is as below. > > > 19960.0000 -6.78192 > 19962.0000 33.3579 > 19964.0000 -3.1808 > 19966.0000 -15.0304 > 19968.0000 -55.4436 > 19970.0000 -38.9422 > 19972.0000 -9.41927 > 19974.0000 -5.95981 > 19976.0000 0.626319 > 19978.0000 2.28736 > 19980.0000 23.5115 > 19982.0000 10.6415 > 19984.0000 -0.233446 > 19986.0000 8.26525 > 19988.0000 36.7656 > 19990.0000 26.6017 > 19992.0000 64.43 > 19994.0000 53.3844 > 19996.0000 18.3834 > 19998.0000 39.8988 > 20000.0000 43.6291 > > I expect the force should be converged. my understanding might be wrong. I > have poor knowledge about this umbrella sampling convergence and image > selection for the PMF calculation. is this fluctuation in force due to > pulling group motion out of box? can you give me some idea about the > selection of images for PMF calculation? I found from the pullx files that > the COM distance converges after few ns of simulation. I understood that we > cant do PMF study with pull=constraint. > > Vijay. > > >> Message: 2 >> Date: Mon, 07 Nov 2011 09:07:21 -0500 >> From: chris.ne...@utoronto.ca >> Subject: [gmx-users] umbrella sampling with "pull=constraint" >> To: gmx-users@gromacs.org >> Message-ID: <20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca> >> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; >> format="flowed" >> >> Dear Vijay: >> >> Can you please provide evidence for your claim that the harmonic >> potential is not applied properly, since you may decide to use >> pull=umbrella once you have set that up correctly. Importantly, >> movement out of the unit-cell is not a problem, as discussed a lot on >> this list. Nevertheless, you do need to worry about which images are >> used to derive the pulling forces. You can often do that by a >> judicious selection of pull_pbcatom (read about that on-list and in >> the manual). In some cases, however, pull_pbcatom can not assist >> enough and you are forced to make the box larger. None of this is >> alleviated by pull=constraint, which is why I'm not going to answer >> your question about your .mdp parameters at this point. Let's get the >> problems identified and solved first with pull=umbrella. >> >> Chris. >> >> >> -- original message -- >> >> Hello, >> >> I have done umbrella sampling with "pull=umbrella" and I found that the >> pulling group has high fluctuations and sometimes moving out of the >> periodic box. I think that the harmonic potential is not properly applied >> and thus the pulling group is not retained with the specified COM distance >> between the reference and pulling group. Can we use pull=constraint option >> to retain the pulling group within the COM distance? my pulling code is as >> bellow with restrain at 0.5nm distance from ref group. I just want to get >> some idea about this pull code modification. >> >> pull = constraint >> pull_geometry = distance >> pull_dim = N N Y >> pull_start = no >> pull_ngroups = 1 >> pull_group0 = Chain_A >> pull_group1 = Chain_B >> pull_init1 = 0.50 >> pull_rate1 = 0.0 >> pull_k1 = 1000 >> pull_nstxout = 500 >> pull_nstfout = 500 >> >> >> Regards, >> Vijay. >> >> >> >> - >> > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
