[gmx-users] Parameterising for a Solvent

[David]

On Wed, 2003-09-03 at 04:34, Dallas Warren wrote:
> David,
> 
> > >         DHvap = 43.21           versus 58.0
> > You're saying that it is 14.7 kJ/mole off? Hmm, what molecule is
> > this?
> 
> Yes, that is what I have gotten from the liquid and gas calculations. 
> Propylene glycol or 1,2-propanediol.  
> 

> Thank you for the references.  They have been a great help.
> 
> Is the parameter coupling an active feature of the current release of
> GROMACS?  Been through the manual a couple of times, searched the site
> etc. and haven't been able to find any mention of it.

Yes, just pass an an extra file (xx.gct) to mdrun. The format is a bit
odd:

;
;	File 'bam.gct' was generated
;	By user: spoel (291)
;	On host: carr
;	At date: Mon May 15 22:21:54 2000
;
Pres            =            1  ; Reference pressure for coupling
Epot            =        -41.7  ; Reference potential energy
Dist            =        0.275  ; Reference distance
Mu              =          3.6  ; Reference dipole
Force           =            0  ; Reference force
Fx              =            0  ; Reference force in X dir
Fy              =            0  ; Reference force in Y dir
Fz              =            0  ; Reference force in Z dir
Px              =            0  ; Reference pres in X dir
Py              =            0  ; Reference pres in Y dir
Pz              =            0  ; Reference pres in Z dir
Polarizability  =            0  ; Polarizability used for the Epot
correction
Dipole          =            0  ; Gas phase dipole moment used for Epot
correction
Memory          =            1  ; Memory for coupling. Makes it converge
faster.
UseEinter       =           no  ; Use intermolecular Epot only (LJ+Coul)
UseVirial       =           no  ; Use virial iso pressure

; Q-Coupling     type            xi

;   Couple       To  i-type  j-type         xi-c6        xi-c12
; j-type == -1 means mixing rules will be applied!
LJ       =     Pres       0       0             0          1000
LJ       =     Epot       0       0         -1000             0

;   Couple       To  i-type  j-type          xi-A          xi-B         
xi-C
; j-type == -1 means mixing rules will be applied!

; More Coupling


The reference stuff is important (Epot and Pres) and the coupling
constants under Q-coupling and LJ-coupling.

If you want to give it a go you can contact me off the list.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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