[gmx-users] lipids in force field

André Farias de Moura moura at ufscar.br
Wed Apr 6 16:42:32 CEST 2016

Hi Yao,

Not really sure if that's what you asked, but general purpose FF usually
specify bond lengths for specific molecular fragments/molecules without
considering the specific phase into which that molecular fragment/molecule
might be in.

>From the standpoint of statistical mechanics, you should consider the
change in the partition function as the system undergoes a phase change,
but the relevant property would be the vibrational frequencies of the
bonds, not their lengths, so I cannot see the point of minding about bond

You should also mind that bonds including H atoms are ill-defined both
experimentally and from the standpoint of classical FF, since they are
intrinsically quantum mechanical and classical approximations fail to
describe them properly.

As regards the simulation of phase transitions, I never did it myself, but
I guess that you should mind about things other than bond lengths for such
a phase transition. For instance, deuterium order parameters measure how
the tails become more/less orderly as the phase changes (which is typically
done for these phase transitions). Although we attribute the order
parameter to specific atoms within a molecule, you should mind that it is
not a single-molecule property, since the same lipid molecule will undergo
that change in its order parameters depending on its more/less orderly
environment (it is a property of the phase, not of the single molecules).

I hope it helps.


On Wed, Apr 6, 2016 at 10:15 AM, xy21hb <xy21hb at 163.com> wrote:

> Dear all,
> Just a general question, is the bond lengths of a lipid in a force field
> in liquid phase or in gel phase?
> And how could one simulate the phase transition with the pre-determined
> bond parameters?
> Best,
> Yao
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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