Re: [gmx-users] RDF calculation from surface of protein

-surf flag is used with -ref flag. Provide the reference file in the -ref flag. On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash wrote: > Hi all, > > I am trying to calculate the RDF between the protein surface and the > centre of mass of my ligand and water molecules. Please find below the >

Re: [gmx-users] rdf calculation for wormlike micelles

Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line

Re: [gmx-users] rdf calculation for wormlike micelles

You cannot use a line as the reference. From a brief glance at the paper you link it seems like maybe you actually want to compute the expectation value of the micelle backbone, a method known as principle curves which is a generalization of principle component analysis. At any rate, you should

Re: [gmx-users] rdf calculation for wormlike micelles

Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line

Re: [gmx-users] rdf calculation for wormlike micelles

See here for info on the selection syntax http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçar wrote: > Dear all, > > I am working on a wormlike micelle that has a curved structure. I want to > calculate the

Re: [gmx-users] RDF calculation.

Well, since you are not interested in the duplex stability, I would not use -COM. See, during the simulation, the center-of-mass of such a small helix part can drastically move, leading to a questionable result. Check your system and make sure that you will not face this situation. About the PMF,

Re: [gmx-users] RDF calculation.

On 12/27/14 4:17 AM, soumadwip ghosh wrote: Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in