[gmx-users] Free energy landscape

[RAHUL SURESH]

Hi users

I find few methods of plotting free energy landscape. Of them one is
plotting rg vs rmsd and another one is using Principe components. What is
the difference in these two methods? Is the plot obtained by both the
method are one and the same?

Thank you
-- 
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

[Shreyas Kaptan]

Sounds like a problem for string methods. However, it's hard to judge
without actually looking at what you have. Cheers.

On Sun, May 13, 2018 at 3:47 PM Rezgar Pakravan 
wrote:

> ​HI there
>
> I got free energy landscape using Mathematica software to get coordinates
> with the least free energy.
>
> 3d image of the landscape shows a gap though!? would that be reliable to
> get coordinates from any point on the lowest energy coordinate
> ?
> any recommendation would be appreciated
>
> Pakravan/Rezgar
> --
> 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.



-- 
Shreyas Sanjay Kaptan
-- 
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

[Rezgar Pakravan]

​HI there

I got free energy landscape using Mathematica software to get coordinates with 
the least free energy.

3d image of the landscape shows a gap though!? would that be reliable to get 
coordinates from any point on the lowest energy coordinate
?
any recommendation would be appreciated

Pakravan/Rezgar
-- 
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

[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
>
> * 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
> | (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 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 

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

[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

==
--
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 | 
(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.

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

[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

==
--
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 | (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.

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

[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
> 
> * 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

[Romero, Raquel]

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

[Romero, Raquel]

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: Protein-Ligand System

[Jacob Babinec]

Hi GMX users,

In order to calculate the free energy of a protein-ligand system, do you have 
to assign different lambda states?


Thank you very much,


Jacob Babinec
-- 
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: Protein-Ligand System

[Justin Lemkul]

On 5/25/14, 4:40 AM, Jacob Babinec wrote:

Hi GMX users,

In order to calculate the free energy of a protein-ligand system, do you have 
to assign different lambda states?



The lambda values supplied in .mdp files are indicators of the extent to which a 
transformation has occurred, i.e. for calculating DeltaG of some process.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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.

Re: [gmx-users] free energy landscape

[Justin Lemkul]

On 11/28/13 7:20 AM, aixintiankong wrote:

Dear, i want to make a free energy landscape with respect to Rg and RMSD.
First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate.
And the i merge the rmsd value and Rg value into one file with two column,
then i use the g_sham command to got the free energy landscapes. does it
right or not? i have seen dihedral PCA from your website (


Yes, that's correct.


http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=landscape),
should i use the g_covar and g_anaeig commands to get the free energy
landscape with respect to Rg and RMSD? if yes, please tell how to do it ,
thank you very much!



g_covar and g_anaeig are necessary in that case to extract the data of interest; 
those programs have no bearing on what you are doing.  The process is identical 
though - generate a text file of the two variables of interest (for 
g_covar/g_anaeig, the columns are eigenvalues) and then plot with g_sham.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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.