[gmx-users] [Fwd: a question about your reply]

[Yang Ye]

On 7/4/2007 4:56 PM, Mark Abraham wrote:
> Please keep conversations on the list in case others want to contribute,
> and so the outcomes are stored for others to search for.
>
> I thought I answered your current question when I observed that the
> deviations you observe seem normal. The size of these deviations will
> depend on the nature of your system and how much thermal energy is going
> around. Nobody is likely to think anything of a few degrees. The molecular
> mechanics approximation isn't going to reproduce geometries to closer than
> that sort of difference anyway.
>   
You may use all-bonds (bonds and angles) for constrains to reduce 
high-frequency motion for bonds, but for torsional, your result is alright.

The inter-atomic interaction in force fields are merely model, which 
doesn't necessarily to bear physical meaning. Bond and angle in force 
fields may find their counter-parts in quantum mechanics but they are 
still different. Torsional is primarily to correct the remaining energy 
or to constrain certain structure. Having small fluctuation means that 
such correction is working well.
> Mark
>
> ---------------------------- Original Message ----------------------------
> Subject: a question about your reply
> From:    ÀïÃÎ <limeng9505 at tom.com>
> Date:    Wed, July 4, 2007 6:37 pm
> To:      mark.abraham at anu.edu.au
> --------------------------------------------------------------------------
>
> Dear Mr Mark,
>    Thanks very much for your reply, but I think I did not describe my
> question clearly in my last letter.
>  I know the value will move around the minimum defined at 120 degrees when
> using harmonic potential and the dihedral will deviate from 120 degrees
> during the simulation, but I don't know what magnitude of deviation is
> proper for the simulation. For example, in my simulation, the maximum
> deviation is 2 degree, is it too big or proper? Or should I
> control the maximum deviation as small as possible?
>
>
>
>
>
>
>                                                           Meng Li
>  2007.7.4
>
>
>
>   
>
> ------------------------------------------------------------------------
>
> Dear Mr Mark,
> Thanks very much for your reply, but I think I did not describe my 
> question clearly in my last letter.
> I know the value will move around the minimum defined at 120 degrees 
> when using harmonic potential and the dihedral will deviate from 120 
> degrees during the simulation, but I don't know what magnitude of 
> deviation is proper for the simulation. For example, in my simulation, 
> the maximum deviation is 2 degree, is it too big or proper? Or should I
> control the maximum deviation as small as possible?
>
>
>
>
>
>
> Meng Li
> 2007.7.4
>
>
>
>
>
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