[gmx-users] Parameterising for a Solvent

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Sep 2 09:39:01 CEST 2003

Thank you for the replies Eric and David.

I was hoping it was something as simple as that :-)

I have performed a single molecule simulation.  If only all simulations 
went that quickly ;-)

>DHvap = (Eintra(g) + RT) - (Eintra(l) + Einter(l))

Thank you, that makes sense now.

>The second bit is your Epot in the liquid sim, then you have to compute
>Eintra(g) by running a simulation of a single molecule *IDENTICAL* to
>your liquid simulation. In particular when you use PME this will give a

Only difference is that you can't use pressure coupling, correct?  In doing 
so, the box would rapidly contract below twice the cut off length.

>very large number. Take care to run the single molecule at least as long
>as the liquid simulation as you will have rather large fluctuations in
>energy. See further Wensink et al. (JCP 119, no 13, to be published).

The liquid simulation I have run for 3 ns so far.  With the single molecule 
simulation I found that when the dihedral underwent a conformation change 
to the higher energy state the various energy terms increased quite 
significantly.  So I have run that for 50ns for the value calculated below.

OK, having done that now:
         Eintra(gas) = 55.4815
         RT = 2.4776
         [Eintra+Einter](liquid) = 14.747
         DHvap = 43.21           versus 58.0

Now that is much more reasonable.  Not perfect, but at least in the ball 
park now.

Something to note here, which isn't surprising but I hadn't thought of it 
that way, changing the L-J values will have little influence on the 
potential energy of the gas phase.  The value of that in this case is 
dominated by electrostatic short range and electrostatic 1-4 interactions.

Thing is now, which way to go to improve the value?  Redistribute the 
partial charges (which I assume will have a significant effect on the gas 
phase potential energy and is the dominate term)?  Decrease the minimum in 
the L-J potential to decrease the value of the liquid phase potential energy?

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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