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
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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.
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
Pakr
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 simulatio
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 fil
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 eigenvalu
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 wrot
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
coord
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 show
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
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 c
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
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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 comman
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. do
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