[gmx-users] amber99 with berger's lipids
jmsstarlight at gmail.com
Wed Apr 10 07:42:32 CEST 2013
first of all I think that something wrong in amber and charm simulations
because of some fluctuations of the box x-y-z dims during simulation
Energy Average Err.Est. RMSD Tot-Drift
Box-X 9.32108 0.0068 0.0360834 0.0289953 (nm)
Box-Y 8.89245 0.0064 0.0344241 0.0276619 (nm)
Box-Z 9.07051 0.013 0.0702945 -0.0525563 (nm)
so due to decreasing of the box dims the overal conformational behaviour of
the system is very 'straitjacketed' - its likely my protein placed in the
compact crystal environment preventing its dynamics.
2013/4/9 Mark Abraham <mark.j.abraham at gmail.com>
> On Tue, Apr 9, 2013 at 9:59 AM, James Starlight <jmsstarlight at gmail.com>
> > By the way during simulation of the membrane-protein systems in the
> > Amber99sb ff (with berger lipids) I've noticed decreased of my system in
> > the Z-direction ( I've observed the same also during simulation of such
> > systems in the Charm full atomic ff). In both cases the observed effect
> > seen in both GPU and non-gpu regimes with different cutoffs.
> > It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff
> > with berger lipids) I didnt observe such decreasing in the Z - dimension
> > my bilayer. The only difference was in the water models (spc in the
> > and tip3p in the amber or charm). Might it be relevant ? Should I switch
> > the spc water with the amber ?
> On principle, that is a bad idea. The force fields are parametrized to
> work with a particular water model, and you should only use another
> one after careful testing that there is a suitable benefit that
> outweighs any drawback. They are not plug and play.
> You have observed two different systems show different behaviour
> contracting in the Z direction. Why do you think one is abnormal and
> one is not?
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