**From:** Lindong Weng (*wenglindong_at_gmail.com*)

**Date:** Tue Dec 11 2012 - 16:15:55 CST

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Hi, NAMDers,

I have figured out how to get the simulation of pure Ar or Kr fluids

started. Thanks for your help. But I got another problem afterwards, that¢s

about the results. The VdW energy term given by my simulation (~ -952

Kcal/mol or -3978 KJ/mol) is quite different from the literature (~ -5.4

KJ/mol). The total energy did not match neither. And the self-diffusion

coefficient of Ar or Kr atoms is also much smaller than the literature

(0.738 10e-9 m2/s in my study and 2.560 10e-9 m2/s in the literature). But

the density of the simulation system and the RDFs of various atom pairs are

nearly the same as the literature. Is it related to the cutoff I used? I

used cutoff=3.5ó in my simulation but the literature used 2.5ó or even

less. But I found that the difference induced by cutoff value was minor.

Do you have any ideas about the reasons? Thanks in advance.

Below is the force field I used, the parameters for L-J potential were

derived from ó=0.3405 nm and å/êB=119.8 K for Ar-Ar and ó=0.3633 nm and

å/êB=167.0 K for Kr-Kr. I think CHARMM has its own method to calculate

Ar-Kr.

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -

cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5

!adm jr., 5/08/91, suggested cutoff scheme

!

!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]

!

!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)

!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j

!

!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4

!

! ions, note lack of NBFIXes

!

AR 0.0 -0.2381 1.91099 ! Ar

KR 0.0 -0.3319 2.03895 ! Kr

HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use

! READ PARAM APPEND CARD

! to append hbond parameters from the file: par_hbond.inp

END

Lindong

UNC Charlotte

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