[gmx-users] Measuring dihedral energy of various selections

[kobi]

Hi,

may I ask how do you get the potential energies from a simulation? Is it
possible to get continuous energy-time graph for a system?

thanks in advance
Jan Neumann

David Mobley schrieb:
> Maybe this is what someone is getting at in their answers, but you
> COULD sort of "invert" the problem: Use mdrun -rerun to calculate the
> energy of the system WITHOUT the dihedrals you are interested in (i.e.
> by removing these). And then if you subtract the potential energies
> for that from the original potential energies, you'll have the
> dihedral potentials of interest.
>
> David
>
>
> On 8/17/06, Bob Johnson <robertjo at physics.upenn.edu> wrote:
>> Hello everyone,
>> I would like to measure the dihedral energy of certain portions of
>> the same
>> molecule over the course of a previously calculated trajectory. It's
>> important
>> that I get the energy of ONLY these portions. I thought of saving the
>> trajectory of the portion in interest using trjconv. Then using mdrun
>> -rerun to
>> calculate the dihedral energy of this portion. However, this won't
>> work because
>> I would have to make a topology file that contains ONLY this portion.
>> Any
>> ideas?
>> Bob
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