[gmx-users] amber99 with berger's lipids

[Justin Lemkul]

On Wed, Apr 10, 2013 at 1:42 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> Mark,
>
>
> 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.
>
>
I don't see any basis for such claims. You have relatively minor changes in
all dimensions, indicating the box is fairly stable. Depending on how you
constructed the initial configuration, some relaxation in any dimension is
perfectly reasonable. CHARMM is likely the most widely used force field for
membranes; I see no reason to say that using it causes any weird behavior.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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