[gmx-users] Re: using salt in MD

[Graham Smith]

> If one want to simulate under physiological conditions he should use
> NaCl. salt. What artifacts one can get of using or skipping salt in
> simulation?  How to distinguish between aritfacts and truth

I haven't read the papers David mentions but Ibragimova and  Rebecca
Wade did some simulations on a marginally stable WW protein domain,
and found that without salt, or with PME but only enough salt to
neutralize protein charges, the domain unfolded. It was much more
stable with excess salt. 

1: Ibragimova GT, Wade RC. 
    Stability of the beta-sheet of the WW domain: A molecular dynamics
simulation study.
    Biophys J. 1999 Oct;77(4):2191-8.
    PMID: 10512838 [PubMed - indexed for MEDLINE]

2: Ibragimova GT, Wade RC. 
    Importance of explicit salt ions for protein stability in
molecular dynamics simulation.
    Biophys J. 1998 Jun;74(6):2906-11.
PMID: 9635744 [PubMed - indexed for MEDLINE]

########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr