[gmx-users] Parameterising for a Solvent

Erik Lindahl lindahl at stanford.edu
Tue Sep 2 04:38:00 CEST 2003

Hi Dallas,

To find the internal energy I would suggest running a single molecule  
in vacuum.

You will probably get a problem with sampling if it's a small molecule,  
but that can be fixed by using langevin dynamics.

You might also need to use double precision, and either shake with a  
small tolerance, or a lincs_order=8 to get very exact bond constraining  
if you use that.



On Monday, September 1, 2003, at 07:21 PM, Dallas Warren wrote:

> 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 right.
> 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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