[gmx-users] amber99 with berger's lipids

James Starlight 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>
> wrote:
> > 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
> was
> > 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
> of
> > my bilayer.  The only difference was in the water models (spc in the
> gromos
> > and tip3p in the amber or charm). Might it be relevant ? Should I switch
> to
> > 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?
> Mark
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