[gmx-users] Parameterising for a Solvent

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Sep 2 04:31:01 CEST 2003

I am trying to get the parameters right for a solvent molecule.

Appear to have the partial charges right, the dipole moment is within 0.25 
% (2.27 vs 2.276).  Started with similar functional groups in the 
forcefield (G96 43a2x) and made some minor adjustments to get that close.

Managed to get the density pretty good too, within 0.14 % (1035 vs 
1036).  Adjusted the value of L-J parameter V (Cij(6)) slightly to get this 

Problem is that the heat of vaporisation appears to be a long way off 
(-12.2 vs 58.0).  To calculate this (I think this is correct ....), I took 
the internal energy from g_energy (26,545), divided by the number of 
molecules (1,800) to give 14.7 kJ/mol for the internal energy.  Then 
subtracted this value from RT (2.47 kJ/mol), DHvap = -12.2.

To get the correct value of DHvap the internal energy needs to be in the 
order of - 55 kJ/mol.  This seems to be a large difference.  Either I have 
calculated something incorrectly, are using the incorrect method, or the 
parameters are very wrong.

If the former, then where did I go wrong?

If the latter, then I guess I need to change V and W for the L-J potential 
such that the shape of the potential is similar (should preserve the 
density?) but the minimum energy is a fair amount larger (to decrease the 
value of 1-4 LJ and LJ SR enough)?

Thank you for any comments.

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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