Hello,

I am doing research on the melting temp of gold nanoparticles but I am having trouble with obtaining a Root Mean Square Displacement using the fix tmd function. It wants me to have a file with all of the initial coordinates of the atoms in the simulation but I am unsure of how to obtain one. Any advice would really help.

Thank you in advance,

Robert Smith

Hello,

I am doing research on the melting temp of gold nanoparticles but I am

having trouble with obtaining a Root Mean Square Displacement using

the fix tmd function. It wants me to have a file with all of the

initial coordinates of the atoms in the simulation but I am unsure of

how to obtain one. Any advice would really help.

i think you are mixing up stuff here.

fix tmd is performing targeted MD and for that you need to give

a _target_ configuration. this has very little to do with what

you say and what you want. it is not quite clear to me what you

exactly want to use the RMSD for, but you could compute the

MSD with fix msd and then take the square root...

cheers,

axel.