... and everything is segfaulting, though worked perfectly fine until the 'cylinder' thing.
On Wed, Apr 18, 2018 at 3:45 PM, Alex <nedoma...@gmail.com> wrote: > Which then would be = 0 0 1, correct? This though will have to coexist > with pull_coord1_rate = 0.0 > > Is that reasonable? > > Thanks, > > Alex > > On Wed, Apr 18, 2018 at 2:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/18/18 4:08 PM, Alex wrote: >> >>> In addition, we seem to have a different problem: >>> >> >> Cylinder geometry requires the use of pull-coord1-vec, not >> pull-coord1-dim. >> >> -Justin >> >> >> ------------------------------------------------------- >>> Program: gmx grompp, version 2018 >>> Source file: src/gromacs/gmxpreprocess/readpull.cpp (line 234) >>> >>> Fatal error: >>> With pull geometry cylinder the pull vector can not be 0,0,0 >>> >>> >>> On Wed, Apr 18, 2018 at 6:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 4/18/18 3:17 AM, Alex wrote: >>>> >>>> I suppose this question is mostly for Justin... >>>>> >>>>> Let me remind what I am dealing with and ask if my idea is correct. >>>>> >>>>> I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water >>>>> and want to get the Gibbs free energy curve for an ion. For this, I >>>>> have a >>>>> bunch of starting configurations at (X/2, Y/2) and Z varying between >>>>> some >>>>> -z0 and z0. The bias in the "fake" pull mdp is applied as N N Y. Near >>>>> the >>>>> membrane, this means the entire plane is sampled, which adds >>>>> contributions >>>>> I am not interested in. I want the pore and a small region of the >>>>> membrane >>>>> around it, not the membrane, given its properties. >>>>> >>>>> So, I applied weak (k=50) in-plane restraint to the ion for each of the >>>>> sampled configurations -- to keep the sampling region a bit closer to >>>>> the >>>>> pore. The results look completely different, but they finally make very >>>>> good qualitative sense. The ion still walks around within a small >>>>> disk, but >>>>> not much -- this tentatively makes me happy. >>>>> >>>>> Would you believe the results obtained this way, assuming otherwise >>>>> proper setup? >>>>> >>>>> >>>>> This is the exact situation that the "cylinder" pull geometry is >>>> designed >>>> to model. I suggest going that route rather than ad hoc restraints, >>>> which >>>> will influence the PMF and should be otherwise accounted for. >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Assistant Professor >>>> Virginia Tech Department of Biochemistry >>>> >>>> 303 Engel Hall >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> >>>> jalem...@vt.edu | (540) 231-3129 >>>> http://www.thelemkullab.com >>>> >>>> ================================================== >>>> >>>> -- >>>> 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. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> 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.