Project

General

Profile

Task #3306

Document gmx dos tool more clearly

Added by Christian Blau 4 months ago.

Status:
New
Priority:
Normal
Category:
analysis tools
Target version:
Difficulty:
simple
Close

Description

#request

Users on the mailing list stumble regularly over the dos tool and do not know what the output means, specifically if the heat capacity is the c_v or c_p.

In the code the output quantity is named cP, but from reading through the source code it is likely c_v.

More details about the implementation are found in https://pubs.acs.org/doi/10.1021/ct200731v


- I'm trying to calculate the specific heat of my system (specifically, c_p) using gmx dos, and I was curious about how exactly gmx dos calculates c_p. I can't seem to find any documentation anywhere about what formulas are used; all I can ascertain from the gmx dos source code is that it involves integrating the diffusion and solid components of the density of states (each multiplied by some weighting factor). Any help would be greatly appreciated.

- I have found density of states (Dos) of a protein ligand system from gmx dos command of gromacs. I would like to know if it employs the same principle component analysis as used in g_covar. If not what are the differences. 

- Also the Dos obtained from gmx dos has solid and diffusive components, please can anyone shed light on what are they exactly?

Also available in: Atom PDF