<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Hi<br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt; color: rgb(0, 0, 0);"><div><br>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.<br><br>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 ?<br><br>rtpi(nm) chemical potential<br>1 -0.0727196<br>4 -0.0009074<br>7 -0.0001692<br><br>Thanks<br>Pranay
Doshi<br></div>
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