[gmx-users] Free Energy Landscape- PCA

[Mark Abraham]

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.12 at 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 <jalemkul at vt.edu<mailto:
> jalemkul at 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 <jalemkul at vt.edu<mailto:
> jalemkul at 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.12 at ucl.ac.uk<mailto:raquel.romero.12 at 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
>
> jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at 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-request at 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
>
> jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at 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-request at gromacs.org<mailto:
> gmx-users-request at 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-request at gromacs.org.