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I was just wondering if someone here knows the reason for the value used
for the CH2-CH2 dihedral in the GROMACS force field?<br><br>
I have been doing some simulations containing bile salts, which have a
short hydrocarbon chain attached to essentially cholesterol. The
chain was too straight, so I started to look into why this would be the
case. A simulation of 100 decane molecules showed chains that are
very straight with only one, may be two gauche confirmations per
chain. Something isn't looking right here ;-)<br><br>
So, then looked for a paper on the energies of a CH2-CH2 dihedral, pulled
Allinger et al. J. Chem. Phys., 106(12) (1997) which is "The
torsional conformations of butane: definitive energetics from ab initio
methods". The difference in energy between the anti and gauche
conformations is 0.62 kcal/mol. I performed an energy minimisation
of butane in the anti and gauche confirmations and found that the energy
difference using the GROMACS forcefield is 1.58 kcal/mol! The
energy for the dihedral is over twice of what it really should be, no
wonder the chains are straight!<br><br>
How was the value decided on? It just seems to me that is a huge
difference, even if the force field isn't meant for hydrocarbons,
proteins/amino acids still contain chains of CH2-CH2 and those sections
are going to be too rigid.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy<br>
Monash University<br>
381 Royal Parade<br>
Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9076</html>