[gmx-users] Mixed solvents

[Daan van Aalten]

Hi

... furthermore ... - please note that the PRODRG server actually already
does this - the molecule you see rotating after your server run *IS*
actually minimized with GROMACS in vacuum. I.e. PRODRG uses GROMACS for
coordinate generation. Thus - if your molecule "explodes" it more likely
has to do something with your input into gmx, rather than the topology -
you would have seen it "exploding" on the PRODRG server otherwise!

Daan

On Thu, 15 Dec 2005, Dallas B. Warren wrote:

> > The problem is
> > that during the minimization the Taurines are exploding. It seems as
> > they are not kept toghether by their .itp topology included
> > in topol. top
>
> Start by simulating a single taurine molecule by itself in vacuum.  Then
> you can work out what it is unstable, what the problem is with the
> topology etc.
>
> Catch ya,
>
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9073
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
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Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk