Thank you Justin. Right now I have a sodium with three ligand residue. One of the ligand residue is in a not very good position. I would like to apply a soft harmonic distant restraint to keep them together and pull the "bad" ligand residue a little closer. Mostly I am trying to maintain and optimize this sodium-ligand cluster. What would you suggest? I am using Gromacs 5.0.4. The "flat bottom restraints" and "intermolecular distance restraints" are in the 5.1 version? Is "Any pull rate of zero maintains a specified distance using a harmonic biasing potential. " what I need?
Thank you so much!!!! Victor On Tue, Sep 1, 2015 at 2:50 PM, Justin Lemkul <[email protected]> wrote: > > > On 9/1/15 5:44 PM, Victor Ma wrote: > >> Hello Justin, >> >> Thanks for the response!! I know how to set up the pull code. But using >> pull code ("umbrella") would keep pulling the two together causing >> unwanted >> clashes and non-physical scenario. How can I get around with that? >> > > No, it wouldn't do that, but that's besides the point. > > If I set the pull-coord1-rate = 0 and pull-coord2-k = 100, for example, is >> this equal to a harmonic distance constraint without the "pulling" part? >> >> > Any pull rate of zero maintains a specified distance using a harmonic > biasing potential. That's really what the "pull" code is - an external > bias. People often confuse this and think that is *must* induce some net > change, but in fact it doesn't have to. > > I don't really know what your goal is here, but there are lots of ways to > get around this - flat bottom restraints, intermolecular distance > restraints, pull code, etc. If you explain what you actually need to do I > can probably be more specific with how to do it. But a simple restraint > really is just that - simple. > > -Justin > > > Thanks again!! >> >> Victor >> >> On Tue, Sep 1, 2015 at 2:27 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 9/1/15 2:54 PM, Victor Ma wrote: >>> >>> hello all >>>> >>>> I need to apply a distance restraint between a sodium and a residue. I >>>> read >>>> the manual, etc, which seems to suggest adding something like below to >>>> the >>>> .itp file. >>>> >>>> [ distance_restraints ] >>>> ; ai aj type index type’ low up1 up2 fac >>>> 10 16 1 0 1 0.0 0.3 0.4 1.0 >>>> 10 28 1 1 1 0.0 0.3 0.4 1.0 >>>> >>>> But my protein and ions are in two separate itp file. So how do I do it? >>>> >>>> Also I have multiple sodiums, but in the SOD.itp file, there is only one >>>> line >>>> [ moleculetype ] >>>> ; name nrexcl >>>> SOD 1 >>>> >>>> [ atoms ] >>>> ; nr type resnr residu atom cgnr charge mass >>>> 1 SOD 1 SOD SOD 1 1.000 22.9898 >>>> ; qtot 1.000 >>>> >>>> So how do I get the atom number for the specific sodium I want to >>>> restraint? >>>> >>>> >>>> Either you need to use the pull code (simple harmonic restraint) or if >>> you >>> need the flat-bottom nature of the distance restraints, you need to place >>> the [distance_restraints] directive under an >>> [intermolecular_interactions] >>> directive and use global atom numbers. This feature is only available in >>> version 5.1. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> [email protected] | (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 [email protected]. >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (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 [email protected]. > -- 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 [email protected].
