[gmx-users] Influence of rtpi on chemical potential

Pranay Doshi pran_160589 at yahoo.co.in
Thu Feb 17 16:46:22 CET 2011


I am relatively new to gromacs and molecular dynamics simulations. I am trying 
to simulate a system of  1000 Argon atoms in an NVT ensemble in a cubic box of 
size 18.7886 nm(density 10kg/m^3) and temperature 90K. To do this, I have 
assumed that Argon interacts by Lenard-Jones(12-6) potential.

My aim is to find the chemical potential. I use tpi and tpic to find this. I 
have performed energy minimization first and then equilibrated for a period of 1 
ns(with 1 step=1fs) and then I simulate the system for 20 ns after which I do 
tpi/tpic on the trajectory from the 20 ns simulation. But, I noticed a thing 
while comparing tpi and tpic: when I increase rtpi from 1nm to 4nm, the chemical 
potential value changes by a factor of approximately 64(4^3),from 1 to 9 it 
changes by 729(9^3). I have kept nsteps = 100000 and nstlist = 5. This happens 
for both tpi and tpic.So, am I doing something wrong here or is there any volume 
related normalization issue ?

rtpi(nm)    chemical potential
1                   -0.0727196
4                   -0.0009074
7                   -0.0001692

Pranay Doshi

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