[gmx-users] Degrees of freedom for each atom ?

diptipotdar dipti_potdar at hotmail.com
Tue Apr 15 15:19:01 CEST 2014


Hi ,
Is there any option in GROMACS to calculate degrees of freedom for each atom
?
I am using constraints (LINCS-all bonds) in my MD simulation for ligands and
water(SHAKE).
I can see the total degrees of freedom from .log file. .But I am supposed to
calculate the temperature of each atom in a group by using equipartition
theorem by using velocities and masses.
Is there any such option which will help me to calculate individual
temperatures or degrees of freedom for each atom in my system ?
My system contains metal cluster with ligands and water( as a solvent).The
metal cluster is heated by thermostat and I am looking at heat transfer from
metal cluster.

Thanks. 
-Dipti

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