[gmx-users] Parameterising for a Solvent

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Sep 3 04:36:02 CEST 2003


> >         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.

(I have searched around looking for those that have simulated it 
previously, and I get the feeling someone should have, but I can't find any 

>What you may need to do is to increase the dipole (like e.g. spc water
>has 2.25 iso 1.85) to account for polarisation. You can actually
>optimize the parameters during an MD simulation by coupling the
>parameters to the energy and the pressure. Since there are two
>observables you have two degrees of freedom, i.e. you can scale the
>charges to account for higher DHvap, and one of the C12 parameters to
>get the pressure right. See e.g. JCP 108 pp. 10220-10230 (1998) and
>JPC B. 105 pp. 2618-2626 (2001) (pdfs available from my website below)

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.

Catch ya,

Dr. Dallas Warren
Research Fellow
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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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