[gmx-users] potential energy of only the protein

[David Mobley]

Hi,

Depends on what you mean by "the potential energy of only the
protein". The protein alone in what environment? (And what do you hope
this will tell you?)

One thing you can do -- assuming this is what you want to do -- is
strip out all of the waters and then use mdrun -rerun to evaluate the
potential energy of the protein in vacuum. Of course, that tells you
the energy of only the protein in vacuum. If that's not what you want,
then it won't be helpful.

A word of warning: In general, the potential energy of a system (or a
protein) is a quantity that fluctuates strongly. If you are trying to
draw conclusions by looking at, say, the change in total potential
energy of the protein or of your system, this probably will not work,
as the fluctuations will be larger than the change. You can assess
this using error analysis taking into account the autocorrelation
time.

Best wishes,
David


On 30 Oct 2007 10:46:37 -0000, sarbani chattopadhyay
<sarbani_c84 at rediffmail.com> wrote:
>
>
>
>  hi,
>    I want to get the potential energy of only the protein ie. without that
> of the
>  water.'g_energy' calculates the energy from the energy file. The groups
> written for the
>  "energygroups" are 'protein sol'.
>  Is there any way to get the energy only of the protein?
>
>  Thanks in advance.
>
>
>
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