[gmx-users] binding energy calculation when appear this error: no distance restraints in topology

[Justin Lemkul]

On 4/15/13 3:01 AM, fatemeh ramezani wrote:
>
>
>   Dear Justin
> I thought by use of  -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me?

That is not what -pairs does, per the help description.  If you want the energy 
of different components of the system (i.e. residues), you need to set 
appropriate energygrps in the .mdp file such that short-range nonbonded terms 
are decomposed.  If you did not do this in your simulation, create a new .tpr 
file with appropriate groups and re-calculate the energies using the original 
trajectory with mdrun -rerun.  Doing so does not decompose long-range terms 
(i.e. PME).

-Justin

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

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