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

**Date:** Tue Dec 11 2012 - 13:43:16 CST

**Next message:**Gianluca Interlandi: "Alchemical transformations and DDG of point mutations"**Previous message:**francesco oteri: "Re: REST or RESTMD in NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

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

**Next message:**Gianluca Interlandi: "Alchemical transformations and DDG of point mutations"**Previous message:**francesco oteri: "Re: REST or RESTMD in NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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