On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 11/24/17 3:32 PM, rose rahmani wrote: > >> I attached md_pull.mdp file >> >> i put " cutoff-scheme = group" beecause of some errors (about energy >> groups) >> > > The use of energygrps has no effect on the physics. You should view > pairwise interactions energies as an analysis method, not something that > you need to do as part of your MD run. Don't base your algorithm choices on > a quantity that is usually meaningless. > > This is what i try to do(part of some literatures); >> 1-pulling the CM of the object along the z-axis—perpendicular to the >> surface of ZnO >> >> 2-Pulling is implemented through a “dummy particle” which moves towards >> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0 >> and drags the CM by the harmonic force corresponding to the spring >> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so >> the PMF is averaged laterally >> >> 3-The conformations are scanned every 0.1 ps in order to save them >> with the CM within each of the interval of width 0.05 nm. ( most of >> all i'm not sure about this part of my mdp file and i don't know how >> should i implement them). >> > > I don't know what .mdp setting you're referring to here. > > Sorry, I didn't understand what you mean? > > 4-between 36-38 conformations should be collected and i dont know how >> should i choose them between 710 conf.gro files( i got 710 >> conformations after using trajconv) >> > > Calculate the COM distance between the groups for each frame. This is what > my tutorial does and what my provided scripts help you to analyze. Compile > a list of the COM distances and determine which frames are suitable for > starting points of each window. > > -Justin > > > this is first part of my job. >> >> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment. >> >> what do you think about mdp file? where did i make a mistake? >> >> Thank you for your attentions (like always ;) ) >> >> Best Regards >> >> >> >> >> >> Sent from my iPhone >> >> On Nov 24, 2017, at 19:34, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 11/24/17 9:14 AM, Rose wrote: >>>> Hello >>>> >>>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its >>>> tutorial with MR Lemkul) But I don't know how should I implement deltaZ and >>>> how choose different conf.gro and which will be useful for further >>>> sampling. >>>> To tell the truth I couldn't get summary.dat by "perl distance.pl" >>>> command.as I'm not good in programming I couldn't understand what >>>> happened there?! >>>> >>> Run gmx distance manually. It's probably returning some error, so the >>> script fails. I've heard this reported a number of times and no one's ever >>> told me what the solution is, so unfortunately there's nothing I can do to >>> fix it. >>> >>> How did you know for example: >>>> 50>>>0.6 nm >>>> 100>>>0.8 nm >>>> >>> This is what gmx distance computes. >>> >>> I need deltaz=0.05nm >>>> >>> Then you will need to save frames very frequently. This is a very narrow >>> dz, and may be overkill depending on what the system is. >>> >>> Please help me, i don't know where should i find these informations and >>>> modify them. >>>> >>>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm >>>> far from it (and rvdw and coulomb=1.5 and >>>> >>> What force field uses such a cutoff? Don't make ad hoc changes to the >>> cutoffs used by any given force field, as you will get unexpected (or >>> invalid) results... >>> >>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer >>>> to wall(4nm far from slab) except slab. >>>> What is my mistake?! >>>> >>> You'll have to provide an .mdp file and a complete description of your >>> system, how you constructed it, and what your objectives are. Images would >>> help. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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