[gmx-users] analysis of different groups with g_energy

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 10 16:07:36 CEST 2008

Peyman Yamin wrote:
> Good day!
> Thanks for the comments, but maybe it could be done in a less laborious way as 
> following?
> g_energy gives all the interactions between MOL and SOL other than bonding 
> ones. since there is no bond between MOL and SOL, one could do a ONE step 
> simulation of MOL with its last acquired structure from solvent in vacuum 
> and - since it's the whole system now - use g_energy again to get Angle and 
> Dihedral energies. The only problem would then be the Bond itself 
> (stretching) which is not important since when the MOL itself is the whole 
> system, one could even use the tot-energy directly from the one-step MD in 
> vac and by substracting get even the stretching energy.

That seems at least roughly equivalent. Laborious is a subjective 
judgement and depends what technique you would use to do it :-)

> should this be at least OK in a qualitative way. (?)
> Despite of a good discussion on the topic (march,2008 - David, Xavier, Pascal, 
> Berk), I still can't find what contributes exactly to SR,LR and 1-4 
> non-bonding interactions and what does not, other that what they stand for ;) 

I said last time that the place to look for how these might be working 
was in the early chapters of the GROMACS manual. The .mdp options you're 
actually using will vary the manner in which these are calculated.

> are they really independent and additive to give the whole interactions? 

Did you try adding them up?

> or 
> for example the Reaction Field corrections appliy to some and to some not?
> But as far as I FEEL, they are in a good way, so that one can do as above (at 
> least with a reasonably small error).

> If it's not supposed to work from the beginning, i.e. the terms are not 
> additive at all, please let me know! as well as if one should add/substract 
> some things!

First, try to understand the algorithm you're implementing. Then you 
will have a much better idea what quantities are what.


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