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. > > > > - >
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