Re: [gmx-users] free energy landscape

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 >

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

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

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

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

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

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 wrote: > > > > On 12/12/16 9:30 AM,

Re: [gmx-users] Free Energy Landscape: Protein-Ligand System

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

Re: [gmx-users] free energy landscape

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