On 6/2/17 4:17 PM, Alex wrote:
So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
I find that surprising. Please provide the full, exact error and your pull
settings. All of the geometries should work with zero or non-zero pull rates.
But I admit, it has been many years since I used GROMACS with the pull code.
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?
You might get some windows that conveniently work with "simpler" settings but I
still think you need to do what I said before. Old GROMACS versions had a
"position" geometry that was the go-to for membrane/slab/layered systems and
worked quite nicely, but that's gone now, replaced by other options that I've
never used.
-Justin
Thanks,
Alex
On Fri, Jun 2, 2017 at 11:26 AM, Alex <nedoma...@gmail.com> wrote:
Yes, because if your ion diffuses laterally (or whatever constitutes your
"hole"), then you're not sampling what you think you're sampling. That's
what the cylinder geometry is for. You have a system capable of
significant lateral movement, so if you fail to apply a bias that acts in
the x-y plane, your results are very quickly going to become garbage.
-Justin
Of course. I actually realized that you used COM distance and not e.g.
direction-periodic (which won't accept zero pulling rates anyway) only
after I asked.
Specifying somewhat awkward structures like disks as references could be
avoided by simply allowing a component of the COM distance vector and not
the entire vector) to be used. Anyway, doesn't really matter.
Thanks,
Alex
--
==================================================
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
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.
