Re: [gmx-users] Free Energy Landscape- PCA

2016-12-15 Thread 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  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 > 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 > 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
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>
>
> --
> ==
>
> 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
>
> ==
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Re: [gmx-users] Free Energy Landscape- PCA

2016-12-15 Thread Romero, Raquel 
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 
> 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 
> 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

==
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--
==

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

==
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Re: [gmx-users] Free Energy Landscape- PCA

2016-12-15 Thread Justin Lemkul 



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  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

==
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--
==

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

==
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Re: [gmx-users] Free Energy Landscape- PCA

2016-12-15 Thread Romero, Raquel 
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  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
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