[gmx-users] Density of water, Dispcorr and rmsd
Mark.Abraham at anu.edu.au
Wed Mar 9 13:19:58 CET 2011
On 9/03/2011 10:43 PM, Kavyashree M wrote:
> Dear users,
> What is the difference between densities predicted by tip4p and
> spc models?
> I am using tip4p (with OPLSAA forcefield) in the simulation, during
> position restrained
> dynamics, Average water density is around 1015kg-m-3 at 300K which is
> quite far from
> expt value..
You're modelling a flexible three-atom two-lone-pair fluid that does
proton transfer and hydrogen bonding with a non-dissociative rigid
four-point three-parameter model. 1.5% error starts to sound OK
actually. If you were actually using position restraints on those water
molecules, then all you are observing is the density of the starting
configuration. Anyway, deviations of up to about 20-30 are expected, and
the size and sign depend on your pressure coupling scheme, the water
model, and what the water model was parametrized to reproduce.
> The Dispersion correction (DIspCorr) is applicable only when we
> use vdw_type = cut off?
> Any known disadvantage of using vdw_type = switch?
Please do your homework reading the (for example) the manual and primary
literature, as suitable.
> What could be the possible reasons for getting quite noisy and not
> equilibrating RMSD
> of backbone during MD simulations?
Non-ergodicity of finite simulations, a broken model, an intrinsically
unstable system, wrong observations, periodicity artefacts, lack of
experience in judging how significant noise is... anything really :-)
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