Re: [gmx-users] g_msd for many molecules

Thanks for this Vitaly and Justin. George The resulting MSD will correspond to the average from individual atoms. Calculating MSD of an individual atom and ascribing it to a [small] molecule, which this atom belongs to, is reasonable. Assuming that averaged MSD from atoms correspond to the

Re: [gmx-users] g_msd for many molecules

Hi, if you want to calculate the MSD of several molecules, say nrmol, without using the -mol option, which I do not know is still broken, you can do this in three simple steps: 1. Convert your trajectory with trjconv and the option -pbc whole 2. Create an index file, that contains groups,

[gmx-users] g_msd for many molecules

Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index file, will g_msd calculate the MSD of the center of mass of them or it will average over all atoms? Thanks George Dr. George

Re: [gmx-users] g_msd for many molecules

On 5/1/13 8:40 AM, George Patargias wrote: Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index file, will g_msd calculate the MSD of the center of mass of them or it will average

Re: [gmx-users] g_msd for many molecules

The resulting MSD will correspond to the average from individual atoms. Calculating MSD of an individual atom and ascribing it to a [small] molecule, which this atom belongs to, is reasonable. Assuming that averaged MSD from atoms correspond to the cluster they form is not. Dr. Vitaly Chaban