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Erik,<br><br>
<blockquote type=cite class=cite cite>A lot of MD force fields have this
problems with aliphatic dihedrals. I would guess that OPLS is slightly
better than Gromos96, which in turn should be better than Gromacs. (The
"gromacs" force field is really Gromos87 with some
modifications mentioned in the manual - we don't try to develop our own
force field, it is too<br>
much religion in it :-)</blockquote><br>
I could imagine that, they are not simple things. And you should be
concentrating on making GROMACS faster anyway ;-)<br><br>
<blockquote type=cite class=cite cite>If you want to stick to united atom
I would recommend either Ryckaert-Bellemans potentials or The Kuwajima
alternative. The R-B potential is already defined<br>
in Gromacs; just change the dihedral type to "3" and make sure
you REMOVE the 1,4 interactions since these are included in this
functional form.</blockquote><br>
Sticking with a united atom FF at the moment. Changed the topology
to include the Ruckaert-Bellemans potential for butane and then minimised
it. It is much better :-) Here are the values FYI:<br><br>
<x-tab> </x-tab><x-tab> </x-tab><x-tab> </x-tab>GROMACS<x-tab> </x-tab>R-B<x-tab> </x-tab><x-tab> </x-tab>Allinger
et al.<br>
diff
anti/gauche<x-tab> </x-tab>6.6
kJ/mol<x-tab> </x-tab>2.9
kJ/mol<x-tab> </x-tab>2.6
kJ/mol<br><br>
Currently have a decane simulation running to see how the relative
populations of anti/gauche go.<br><br>
What do the protein people use for the various CH2-CH2 dihedrals that are
within some of the amino acids when running simulations with the GROMACS
force field? Or is one of the other FF typically used? From
what I can tell, even if there is a single CH2-CH2 dihedral within the
amino acid it will be far more rigid than it should be, and hence not
show the confirmation dynamics that it should. Or am I wrong in my
thinking here?<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>