[gmx-users] Parameterising for a Solvent
spoel at xray.bmc.uu.se
Tue Sep 2 08:16:01 CEST 2003
On Tue, 2003-09-02 at 04:21, 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
> 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?
DHvap = (Eintra(g) + RT) - (Eintra(l) + Einter(l))
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
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).
> 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.
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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