How Larger? I used 1000 -------- Messaggio originale -------- Oggetto: Re: [gmx-users] position restraint single atom Da: Justin Lemkul A: [email protected] CC:
On 2/15/17 9:33 AM, Andrea Spitaleri wrote: > Hi there, > > I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' > respectively, in order to mimic the anchor-like to a solid support. I have > create ad hoc posre.itp file but for some reason the DNA-anchor is moving too > much from the starting position. I would expect more rigidity around the two > atoms. Does it sound strange to you? I mean, I was expecting oscillation of > the > whole DNA but keeping the anchors fixed. Are two atoms too little to get this > kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2. > > Any help/comments on this are welcome. > What about using a larger force constant? Trying to impede the motion of an entire dsDNA using only two atoms as restraints might be difficult to accomplish. -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]. -- 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].
