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-- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/> On Fri, Feb 27, 2015 at 11:13 AM, Adrian Roitberg <roitberg.ufl.edu> wrote: > Hi > > This look good. Just visualize it once in a while to make sure things > are ok. > > Also... If you are using jar not just as a pushing technique, but you > will also compute work to then gte free energies, keep in mind that you > now have TWO springs acting on the system, one for the pull and one for > the restraint on the water. > > adrian > > On 2/26/15 6:13 PM, Joseph Baker wrote: > > Thanks all. Got sidetracked for a couple of days, but I've had a chance > to > > test this out now. What I've done is to find a water molecule in my > system > > that is about where I want to pull towards and then use a combination of > > jar=1 for the pulling and ntr=1 to define restraints on that water to pin > > it in place relative to the protein. I then used parmed to change the LJ > > type (using the addLJType command) of that particular water molecule's > > oxygen and hydrogens to new types with zero epsilon, and used the change > > command in parmed to zero out the charges on those atoms. pmemd.cuda > seems > > to be able to run with this new output parm7 file and I am seeing my > > protein be steered towards that dummy water molecule. Does this procedure > > make sense? > > > > > > -- > > Joseph Baker, PhD > > Assistant Professor > > Department of Chemistry > > C101 Science Complex > > The College of New Jersey > > Ewing, NJ 08628 > > Phone: (609) 771-3173 > > Web: http://bakerj.pages.tcnj.edu/ > > <https://sites.google.com/site/bakercompchemlab/> > > > > On Tue, Feb 24, 2015 at 7:40 AM, Jason Swails <jason.swails.gmail.com> > > wrote: > > > >> On Mon, 2015-02-23 at 18:20 -0500, Joseph Baker wrote: > >>> Okay. My applications are basically 1. pull on the COM a few monomers > in > >> a > >>> filament while restraining monomers at the other end, along the > filament > >>> axis direction and 2. pull a protein that has a domain embedded in a > >>> membrane out of the membrane. So it seems to me in both of those cases > I > >>> will probably want to keep the dummy atom as a fixed point using the > >> ibelly > >>> restraints, unless I am thinking about this incorrectly. However, it > >> looks > >>> like belly style restraints are also not currently supported in > >> pmemd.cuda? > >> > >> Correct. ibelly is not supported in pmemd.cuda (although the > >> functionality to implement it *is* present). An alternative to ibelly > >> is positional restraints, which *is* implemented on the GPU. > >> > >> I agree with Adrian in that ibelly is not really an "ideal" solution > >> here. What happens when your protein naturally tumbles and that dummy > >> particle is now positioned differently relative to the protein? What > >> you can do is tether that dummy atom to some atoms on the protein to fix > >> the pull direction with respect to a constant frame of reference defined > >> by the protein (not the arbitrary Cartesian space). > >> > >> Ideally you would then use constraints to *fix* that particle in space > >> without having the steering force exert forces on other particles. To > >> get pmemd.cuda to do this, you would need to convince it that your dummy > >> particle is actually a hydrogen atom and turn on SHAKE. However, with > >> the exception of water molecules, I don't think the CUDA code supports a > >> single hydrogen having multiple distance constraints through SHAKE, so > >> you may have to play around with a couple options to get it working. > >> > >> HTH, > >> Jason > >> > >> -- > >> Jason M. Swails > >> BioMaPS, > >> Rutgers University > >> Postdoctoral Researcher > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > -- > Dr. Adrian E. Roitberg > Professor. > Department of Chemistry > University of Florida > roitberg.ufl.edu > 352-392-6972 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Feb 27 2015 - 09:30:02 PST