Justin, I considered single ion- pair. sorry for typing mistake (I wrote 4 ion-pairs).
How can I define distance range. ONe more my cation and anion are close in box edges in my equilibrated strucutre. By defining pull_rate1 = -0.01 can cation and anion will come close to each other? Nilesh Does will it affect on results? On Sat, January 1, 2011 2:01 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello >> I am trying to run umbrella sampling for my system. I have system with >> four ion pair (cation and anion) of ionic liquids and 2048 water >> molecules. I am trying to PMF calculation with cation-anion distance as >> a reaction coordinate. I choose cation as group1 and anion group2. Box >> dimensions are 39.222 39.222 39.222 90 90 90 >> >> Durinh equilibratation cation and anion gets dissociate and move far >> from each other (around 7-8 A). Both cation and anion are close to edges >> of the box. I am more interested in structure where cation and anion >> close (around 2-4A).How can I do the PMF simulation to get this >> structure. Can I define pull_rate1 = -0.01 to get cation and anion to >> get close. How can I keep cation and anion at center or if they close to >> the box edges then does the periodic images of the system will >> interact? >> > > You need to define a series of configurations along a pre-defined > reaction coordinate to properly do umbrella sampling. Whether or not you > can converge four independent pairs is questionable, but I've never tried > it. I think I've said this before: simplify your system. Start with one > pair in water and see if you get a sensible answer and understand the > workflow, then build your system up. > > If your umbrella restraint distance is larger than half the smallest box > vector in the pull dimension, the periodic distance is used instead of the > distance directly across the unit cell. Knowing whether or not the > periodic distance will be used comes from proper planning - define the > range of distances that will make up your reaction coordinate, then make > your box at least twice as large (allowing some extra space for > oscillation about your longest restraint distance and pressure coupling, > if applicable). > > All of the conceptual details are described in a tutorial I wrote. It > sounds to me like you're trying to generate a PMF from a single umbrella > sampling window, which cannot be done. > > http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sam > pling > > -Justin > > >> Down I pasted the part of pull code used in my.mdp file. >> >> >> >> Nilesh >> >> >> >> ; Pull code >> pull = umbrella pull_geometry = distance pull_dim = Y >> Y Y >> pull_start = YES ; define initial COM distance > 0 >> pull_ngroups = 1 pull_group0 = EMI pull_group1 = ETS pull_init1 >> = 0.0 >> pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 >> = 1000 ; kJ mol^-1 nm^-2 >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ======================================== > -- > 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 > > > -- 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
