Re: [gmx-users] Free Energy Landscape- PCA
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.
Re: [gmx-users] Free Energy Landscape- PCA
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 > On 14 Dec 2016, at 12:49, Justin Lemkul <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 >> > > -- > == > > 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. -- 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.
[gmx-users] Free Energy Landscape- PCA
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. 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 -- 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.
[gmx-users] Free Energy Landscape- PCA
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. 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 -- 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.
