Hi, The trjconv -drop* functionality is useful here. IIRC it only does a 1D form, but you can do two stages of that.
Mark On Fri, 16 Dec 2016 02:36 Romero, Raquel <raquel.romero...@ucl.ac.uk> wrote: > Thanks a lot, I know how to do it now, so each value given in the > 2dproj.xvg corresponds to a time step of the simulation, right? so if I > delimit the area in the FEL of which I want to know the coordinates i can > extract all the frames that correspond to those eigenvalues by searching > in the file with a awk script for example... > > > On 15 Dec 2016, at 15:11, Justin Lemkul <jalem...@vt.edu<mailto: > jalem...@vt.edu>> wrote: > > > > On 12/15/16 10:02 AM, Romero, Raquel wrote: > Thanks a lot for your reply, Justin. That’s exactly what want but my > problem is that don’t know how, I mean, how can I know that correspondence? > Getting that correspondence is my only problem > > You (presumably) constructed a time series of eigenvalues from gmx anaeig > -proj along PC1 and PC2, after which you constructed the free energy > surface. That means you have a time series of eigenvalues of those > configurations projected onto PC1 and PC2. So after you identify the bin > in the 2-D surface that the configurations fall, then you have a range of > values to which those configurations correspond. Then you just write a > little script that parses the PC1 and PC2 eigenvalue time series and when > it identifies eigenvalues that simultaneously fall inside the limits, print > out the time value. Then apply trjconv. > > -Justin > > > > > > On 14 Dec 2016, at 12:49, Justin Lemkul <jalem...@vt.edu<mailto: > jalem...@vt.edu>> wrote: > > > > On 12/12/16 9:30 AM, Romero, Raquel wrote: > Hi everyone, > > > I have a number of trajectories over which I have conducted PCA using > Gromacs. I have also generated a Free Energy Landscape using g_sham when > the trajectory is projected along the PCs. I would like to know how I can > extract the coordinates of those states of minimum energy shown in the FEL. > > > You'll need to find the corresponding frames by matching the eigenvalues > from the time series. Then you can dump out those frames using trjconv > -dump. > > -Justin > > > Thanks in advance, > > > Regards > > > > Raquel Romero > Department of Pharmaceutical and Biological Chemistry > UCL School of Pharmacy, University College London > 29/39 Brunswick Square > London > WC1N 1AX > > T: 0207 753 5972 > E: raquel.romero...@ucl.ac.uk<mailto:raquel.romero...@ucl.ac.uk> > > > -- > ================================================== > > 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<mailto: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. > > > -- > ================================================== > > 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<mailto: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<mailto: > 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. -- 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.
