Dear All, Reguarding a question I asked below. Does anyone know what the formulei, etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a density matrix. Is it just a count, summation on x-y or other?
Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 08 Nov 2012 11:46:32 +0100 > Von: "lloyd riggs" <lloyd.ri...@gmx.ch> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Re:Ka/Kd > Dear All, > > So I went over the below Ka/Kd...Seems doesnt fit for anything, the DelG I > found doesnt change for components, and just fit my data for the first 20 > analysis by chance I guess, except for Ent and Enth calculations from doing > PCA, which break down nicely. In case anyone reads this. > > I have another couple questions regarding graphing. > > -Regarding the output from g_gyrate, with the -nz option. Is there a > script somewhere to turn the x,y slices into a 3D plot or something (its > around > 40 slices for say an 8 Ang. Z , times each time point. You can do it by > hand, but that turns into plugging the numbers into a matrix by hand for 200 > point per time frame....and most spread sheet things I have used (qti, > Gnu, MS office) dont allow the manipulation of the data properly for such a > plot, as its not simple cut and paste as with most plots. In the end, one > would most likely only need 2-3 snapshots over a run (200 points each) to > show say a density of gyration for extreems, but you would have to look at > most of them visually to find proper ones, especially from multiple runs) > > -the same for ramachondran. I basically want to just turn specific > residues Vs. normal into histograms or a matrix with simple distribution (a 1 > added to each 2D point for each occupancy to plot 3D ramachondrans). This is > not as bad as the gyrate, but still turns into 200 points per simulation, > times 20 or so simulations. I already know grace can take a column and turn > it into a histogram, but not in 2D grids. This I am sure is somewhere (a > script or software), but have no clue whom/where to ask. > > Sincerely, > > Stephan Watkins > > -------- Original-Nachricht -------- > > Datum: Tue, 06 Nov 2012 13:18:48 +0100 > > Von: "lloyd riggs" <lloyd.ri...@gmx.ch> > > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Betreff: Re: [gmx-users] Re:Ka/Kd > > > Thank you for the reply, > > > > Figured. Needless to say though, the software using the pulled gives > > about the same as by hand (although diffusion constants are also guessed > but > > fit into what the computer calculates as compared on a scale of > > lysozyme,,yyyy, xxx, Fab fragments) but can not do the forward/backward > (values of > > -65000.045/-74967.031), while the one way and integral give reasonable > values, > > and the caculated (via g_hbond or g_hbond->g_analyze) DelG fits well > also... > > > > grĂ¼ess > > > > Stephan > > > > -------- Original-Nachricht -------- > > > Datum: Mon, 05 Nov 2012 18:14:36 -0500 > > > Von: Justin Lemkul <jalem...@vt.edu> > > > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Betreff: Re: [gmx-users] Re:Ka/Kd > > > > > > > > > > > On 11/5/12 9:59 AM, lloyd riggs wrote: > > > > Quick question, > > > > > > > > I went and calculated the Ka/Kd with the g_hbond --> -g_analyze and > > just > > > wondered, if all my simulations are pulled, does it in the end make > any > > > sense, or is there ways to compensate for this. I assume the h_bond > > life > > > would be meaningless, as under a normal situation, 2 proteins h-bond > > lifes > > > could stretch into the seconds (minus fluctuation around a very small > > bound > > > area)... > > > > > > > > > > Extracting equilibrium properties from a non-equilibrium simulation is > > > dicey, > > > indeed. I've never attempted such a thing myself, but I would think > > > determining > > > Kd from deltaG would be more reliable, at least inasmuch as the deltaG > > > estimate > > > is reliable (i.e., from umbrella sampling and a proper assessment of > > > errors). > > > > > > -Justin > > > > > > -- > > > ======================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. 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