Re: Argon solvent

From: Jérôme Hénin (
Date: Tue Feb 17 2004 - 12:03:16 CST

Hi Gianni,

If I were you, I wouldn't use reduced units, because NAMD assumes chemist's
units are in use all the way round. I can't swear it won't work, but you'd be
taking a serious risk. And as you point out, it won't be compatible with your
later work, too. And there's not much left to do on pure argon, anyway.

Generating the PSF should be quite a piece of cake. You can write a CHARMM
topology file defining a residue with only one atom - hard to find a simpler
It would look like :
MASS 195 AR xx.xxxxx AR ! need the mass here

DEFA FIRS NONE LAST NONE ! don't want to patch anything

RESI A 0.00 ! net charge is 0
ATOM AR AR 0.0 ! charge on AR is 0
You can load that in psfgen, generate a segment of whatever length you want
and save the psf. You'll have to generate a PDB file with initial coordinates
too - a square lattice will do, or even pseudo-random positions - granted you
minimize your system before doing any dynamics.

And you'll need to add van der Waals parameters in the par file. Just follow
the nicely documented model from CHARMM27 :
!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
C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
                ! NMA pure solvent, adm jr., 3/3/93

I guess that's all. If I've made mistakes or forgotten stuff, or if you need
more help, namd-l and myself will be there.


Le Mardi 17 Février 2004 16:55, Gianni De Fabritiis a écrit :
> Dear all,
> to start with NAMD I would like to set up a simple Argon box in periodic
> boundary conditions with NAMD. For what I understand Argon is not in the
> parameter file.
> The simplest things to do is probably to write directly the pdb, psf and
> parameter files for it, but can I just use reduced units in this case?
> If i want to add a peptide in the simulation, I would have to use again the
> complete parameter file etc, solvate, psfgen, etc. Any suggestion on how
> to do have a Argon solvent using psfgen?
> Many thanks,

Jérôme Hénin
Equipe Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS    UMR 7565
B.P. 239	54506 Vandoeuvre-lès-Nancy Cedex
Tel : (33) 3 83 68 43 95	Fax : (33) 3 83 68 43 71

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