Thanks, Justin. That makes it clear. I have one small question: I do not know how does position restraint algorithm work with other things in gromacs, but doesn't it generate a lot of stress due to slab moving from center to near box boundary despite of position restraints, when -com option is used for refcoord-scaling? If there is a lot of stress, would this stress affect simulation results?
Thanks and Regards, Chetan On Tue, Jun 17, 2014 at 10:01 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/17/14, 10:32 AM, Chetan Mahajan wrote: > >> Any ideas : >> >> 1. why slab is moving despite of position constraints? >> >> > Restraints are biasing potentials; they don't prevent movement. Why is it > necessary that your slab not move? > > > 2. That too, only with "com" option of refcoord scaling...with "all" >> option >> slab does not move... >> >> > Using "all" means the restraint reference for each atom is the original > position in the input coordinates, with respect to every atom individually. > It is more stringent, though it can often be unstable. The "com" option > means the restraint potential is calculated with respect to the COM of the > group of restrained atoms; it is a bit more forgiving, since the COM might > only move slightly, even if there are relatively larger changes in the > individual atomic positions. > > -Justin > > Thanks >> >> >> On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan <chetanv...@gmail.com> >> wrote: >> >> The pics should be seen in the reverse order. Due to sorting by name, >>> "After equilibration" pic occurs first. >>> >>> >>> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan <chetanv...@gmail.com> >>> wrote: >>> >>> Thanks. >>>> >>>> No, same things do not happen when it's a NVT simulation or no mixed >>>> potentials. Also, with mixed potentials in NPT simulation, this things >>>> of >>>> slab moving in one direction (thus following water movement) happens >>>> only >>>> with -com option of refcoord-scaling, *not with -all option for >>>> refcoord-scaling. * >>>> >>>> >>>> I have a crystal slab with equal amount of water on both the sides. >>>> During NPT equilibration (with refcoord-scaling option of -com, not >>>> -all), >>>> some water on side side of the slab enters opposite side due to periodic >>>> boundary conditions I have (say water on the right side of the slab, >>>> crosses boundary of the box and enter the left side of the slab due to >>>> periodic boundaries. Even crystal slab follows this water and move same >>>> distance in the same direction of water movement. Following link shares >>>> pictures of the solvated slab before and after equilibration: >>>> >>>> >>>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa >>>> >>>> I feel, this is not an error, but it is odd. Due to periodicity we have, >>>> output of any calculations will remain the same. Again, with -all >>>> option >>>> for refcoord scaling, this movement of water and slab DOES NOT occur. >>>> >>>> Thanks a lot! >>>> regards >>>> Chetan >>>> >>>> >>>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham <mark.j.abra...@gmail.com >>>> > >>>> wrote: >>>> >>>> Hi, >>>>> >>>>> Repeating myself - simplify things! Do sane things happen with NVT? >>>>> With >>>>> no >>>>> mixed potentials? >>>>> >>>>> Your words aren't making sense to me - you'll do much better with >>>>> pictures, >>>>> making sure you turn on your visualizer's option to show the periodic >>>>> box. >>>>> >>>>> Mark >>>>> >>>>> >>>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan <chetanv...@gmail.com> >>>>> wrote: >>>>> >>>>> Hi Justin, >>>>>> >>>>>> I, actually, do not want to preserve any voids. Initial void that I >>>>>> mentioned is supposed to be filled by water during equilibration and >>>>>> it >>>>>> does so. However, problem is that some or major quantity of water >>>>>> >>>>> moves out >>>>> >>>>>> from one side of the box to enter from the opposite side (obeying >>>>>> >>>>> periodic >>>>> >>>>>> boundary conditions) and crystal slab moving following water movement. >>>>>> >>>>> Thus >>>>> >>>>>> although initially there is almost equal amount of water on both sides >>>>>> >>>>> of >>>>> >>>>>> the slab, we have more water on one side of the slab than the other >>>>>> >>>>> side >>>>> >>>>>> after equilibration. In other words, length of the box on one side of >>>>>> >>>>> the >>>>> >>>>>> slab is more than the other side after equilibration, although it is >>>>>> >>>>> same >>>>> >>>>>> on both sides before equilibration. My dilemma is whether this is due >>>>>> >>>>> to >>>>> >>>>>> pressure coupling or any gromacs thing or due to potentials (mixed >>>>>> buckingham and LJ)? >>>>>> >>>>>> Thanks >>>>>> Chetan >>>>>> >>>>>> >>>>>> On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul <jalem...@vt.edu> >>>>>> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> On 6/12/14, 11:15 PM, Chetan Mahajan wrote: >>>>>>> >>>>>>> Dear All, >>>>>>>> >>>>>>>> I am simulating TiO2 crystal solvated by water and ions like >>>>>>>> >>>>>>> sodium and >>>>> >>>>>> formate. I am observing one peculiar thing, and I would like to >>>>>>>> >>>>>>> rectify >>>>> >>>>>> that. I have initial structure of crystal slab at the center of the >>>>>>>> >>>>>>> box >>>>> >>>>>> elongated in z-direction and almost equal boxlength on both the >>>>>>>> >>>>>>> sides, >>>>> >>>>>> with >>>>>>>> a gap of 1 nm between slab surface and first layer of water close to >>>>>>>> >>>>>>> slab. >>>>>> >>>>>>> This space is kept to avoid water going on the sides of the >>>>>>>> >>>>>>> crystal >>>>> >>>>>> during >>>>>>>> equilibration. This was a minor information. Now, the main >>>>>>>> >>>>>>> observation >>>>> >>>>>> is >>>>>> >>>>>>> that during NPT equilibration, water from one side of the slab >>>>>>>> >>>>>>> enters >>>>> >>>>>> the >>>>>> >>>>>>> other opposite side of the slab (using periodic conditions) so that >>>>>>>> boxlengths on both sides of the slab are very different at the end >>>>>>>> >>>>>>> of >>>>> >>>>>> equilibration. Is this an artifact of pressure coupling? Following >>>>>>>> >>>>>>> is my >>>>> >>>>>> equilibration .mdp file. I have tried varying the compressibility >>>>>>>> >>>>>>> and >>>>> >>>>>> tau-p >>>>>>>> parameters in the following file. e.g. zero compressibility in x/y >>>>>>>> direction or tau-p reduced to 3. >>>>>>>> >>>>>>>> >>>>>>> With pressure coupling, any voids present in the system will be >>>>>>> compressed. If you need to try to preserve some sort of vacuum >>>>>>> >>>>>> layers, >>>>> >>>>>> use >>>>>> >>>>>>> NVT. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>> >>>>>>> Department of Pharmaceutical Sciences >>>>>>> School of Pharmacy >>>>>>> Health Sciences Facility II, Room 601 >>>>>>> University of Maryland, Baltimore >>>>>>> 20 Penn St. >>>>>>> Baltimore, MD 21201 >>>>>>> >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>> >>>>>>> ================================================== >>>>>>> -- >>>>>>> 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? 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? 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. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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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