Re: [gmx-users] hydrogen bond analysis

On 10/29/13 5:46 PM, larif sofiene wrote: Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyse

[gmx-users] hydrogen bond analysis

Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyses hydrogen bond occupancy over trajectory ? My

Re: [gmx-users] Hydrogen Bond analysis using Gromacs

HI, s0, s1,… is (xm)grace codes that refer to the different datasets in the file. Gromacs prints the datasets as different columns. I suggest opening the file with xmgrace -nxy yourxvgfile.xvg. As for the -life option, the results are based on a too wimple kinetic model for most applications.

[gmx-users] hydrogen bond analysis

Dear Users, I have come across a few publications, where they have carried out the hydrogen bond analysis between the two substances. They reported the occupancy percentage of the two substances during the simulation. I really dont have any idea about these. What actually they corresponds to? Is t