[gmx-users] Cluster analysis on molecules

Hi all, I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have to create a separate tpr file for the molecules of interest. I

Re: [gmx-users] Cluster Analysis

... and you can get that file written by gmx cluster. Mark On Thu, Sep 29, 2016 at 12:10 PM Tsjerk Wassenaar wrote: > Hi Sanket, > > gmx trjconv allows writing frames based on a frame index file or using a > xvg file and threshold. Check the help of trjconv on it. > > Hope

Re: [gmx-users] Cluster Analysis

Hi Sanket, gmx trjconv allows writing frames based on a frame index file or using a xvg file and threshold. Check the help of trjconv on it. Hope it helps, Tsjerk On Thu, Sep 29, 2016 at 9:05 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > I performed a cluster

[gmx-users] Cluster Analysis

Dear, gmx-users, I performed a cluster analysis using gmx cluster. I found a total of 178 clusters with the highest cluster having 63 members. I wish to save these members to a .trr or .pdb file in order to perform analysis on all these members as a whole and not on the representative structure

[gmx-users] cluster analysis on HREX results

Dear all, 1. For the cluster analysis, I am using the gromos method with cutoff 0.25 nm. With this cutoff I got 201 structures for the lowest temperature for trajectories that are continuous in time (after using demux.pl) The rmsd ranges from 0.073 to 1.55nm. If I reduce the cutoff to 0.1 nm I