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-- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 On Sun, Jul 9, 2017 at 2:31 AM, Bill Ross <ross.cgl.ucsf.edu> wrote: > And slow down that loop with an if stmt to quit early if atoms overlap. > > Bill > > > On 7/8/17 9:01 PM, Bill Ross wrote: > > Instead of an energy function, you could add up all the atom pair > distances. > > > > Bill > > > > > > On 7/8/17 9:00 PM, Bill Ross wrote: > >> Hi Guqin, > >> > >> Maybe it could be a python script. E.g. start with the first molecule's > >> position as the reference. Then somehow for each other molecule > >> recursively choose a translation (or none) from the neighboring images, > >> finally when all molecules have been recursively assigned, calculate the > >> energy with an available? amber call, storing the min config seen in a > >> global variable. It could be parallelizable. Ok time-wise for a few > >> molecules, but I wouldn't want to do it with the waters in a bath. > >> > >> Bill > >> > >> > >> > >> On 7/8/17 8:34 PM, Guqin Shi wrote: > >>> Hi Bill, > >>> > >>> Could you explain a little bit more about "image minimizer"...my > >>> understanding is to write a small script that try all different orders > of > >>> center-image...? > >>> > >>> Best, > >>> Guqin > >>> > >>> On Sat, Jul 8, 2017 at 10:22 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >>> > >>>> What's needed is an image minimizer that tries all neighboring box > >>>> placements for all molecules. > >>>> > >>>> Bill > >>>> > >>>> > >>>> On 7/8/17 7:06 PM, Guqin Shi wrote: > >>>>> Hi Dan, > >>>>> > >>>>> Thanks for reply. > >>>>> Yes, the first I've thought of is to use "autoimage" directly. I > have to > >>>>> admit it worked unexpectedly well. But for the late ns trajectories, > it > >>>>> failed, too. It has the same result as the one I got from the > separate > >>>>> center-and-image... > >>>>> > >>>>> Best, > >>>>> Guqin > >>>>> > >>>>> On Sat, Jul 8, 2017 at 8:02 PM, Daniel Roe <daniel.r.roe.gmail.com> > >>>> wrote: > >>>>>> Hi, > >>>>>> > >>>>>> Try the 'autoimage' command in cpptraj and see if that works for > you. > >>>>>> > >>>>>> -Dan > >>>>>> > >>>>>> On Sat, Jul 8, 2017 at 6:59 PM Guqin Shi <shi.293.osu.edu> wrote: > >>>>>> > >>>>>>> Dear all, > >>>>>>> > >>>>>>> My simulation is on a huge complex containing 6 molecules. To > visualize > >>>>>> the > >>>>>>> trajectory and get "correct" coordinates, I usually center-n-image > the > >>>>>>> coordinates... I used to center on 1 molecule, image, and then > center > >>>> on > >>>>>> 2 > >>>>>>> molecules (include the first one), and then image; and eventually > >>>> center > >>>>>> on > >>>>>>> 6 molecules and image, as suggested in some amber mailing list > posts. > >>>> It > >>>>>>> worked well. > >>>>>>> > >>>>>>> ex. > >>>>>>> center :1-300 origin (molecule 1) > >>>>>>> image center origin > >>>>>>> center :1-500 origin (molecule 2) > >>>>>>> image center origin > >>>>>>> center :1-650 origin (molecule 3) > >>>>>>> image center origin > >>>>>>> center :1-950 origin (molecule 3) > >>>>>>> image center origin > >>>>>>> center :1-1150 origin (molecule 4) > >>>>>>> image center origin > >>>>>>> center :1-1300 origin (molecule 6) > >>>>>>> image center origin > >>>>>>> > >>>>>>> However, as the molecules deviates during the simulation, after > >>>> applying > >>>>>>> the above commands, there is always one molecule (it could be > different > >>>>>>> molecule dependent on the order I center-image on different > masks...) > >>>>>> that > >>>>>>> just couldn't be placed back... no matter how different > combinations I > >>>>>> have > >>>>>>> tried... > >>>>>>> > >>>>>>> My first question is that does it make sense that the above > commands > >>>> work > >>>>>>> well for first quite a few ns of trajectories but failed to wrap > for > >>>> the > >>>>>>> late ns of trajectories...? > >>>>>>> > >>>>>>> The second one will be if there is any tips or suggestions or > starting > >>>>>>> point that I could try out? I have tried different combinations, > >>>> starting > >>>>>>> center on different molecule(s), I just couldn't get all 6 back to > the > >>>>>>> correct place... > >>>>>>> > >>>>>>> I also tried to center on reference structure...but it just put > >>>> molecule > >>>>>>> onto the geometric center, the direction is still off...I don't > know > >>>> how > >>>>>> to > >>>>>>> center molecules onto a suitable place so that all 6 could be fit > into > >>>>>> one > >>>>>>> box...That doesn't make sense...I mean I start with an intact > >>>> complex... > >>>>>>> Thank you for any thoughts! > >>>>>>> Best, > >>>>>>> Guqin > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> -- > >>>>>>> Guqin SHI > >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>>>> College of Pharmacy > >>>>>>> The Ohio State University > >>>>>>> Columbus, OH, 43210 > >>>>>>> _______________________________________________ > >>>>>>> AMBER mailing list > >>>>>>> AMBER.ambermd.org > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>> > >>>>>> -- > >>>>>> ------------------------- > >>>>>> Daniel R. Roe > >>>>>> Laboratory of Computational Biology > >>>>>> National Institutes of Health, NHLBI > >>>>>> 5635 Fishers Ln, Rm T900 > >>>>>> Rockville MD, 20852 > >>>>>> https://www.lobos.nih.gov/lcb > >>>>>> _______________________________________________ > >>>>>> 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 > >>>> > >> _______________________________________________ > >> 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Jul 09 2017 - 20:00:02 PDT