[gmx-users] analysis of different groups with g_energy

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Tue Jun 10 10:45:06 CEST 2008

Good day!

Thanks for the comments, but maybe it could be done in a less laborious way as 

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.

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 ;) 
are they really independent and additive to give the whole interactions? 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!


On Tuesday 10 June 2008 03:40, Mark Abraham wrote:
> Peyman Yamin wrote:
> > Hi again,
> >
> > Now I remember! some old g_energy let me use numbers as the input for the
> > terms I wanted...!
> Yeah, it changed going from 3.3 to 3.3.1, IIRC. This allowed for scripts
> to be much more general, since the numbers used to change for different
> simulation types.
> > As you say, it looks like the total energy for different groups is not
> > calculated. So I should somehow do it myself? If yes, I don't even know
> > where I should get the terms I should add together from? I think I'd need
> > all bonding and nonbonding interactions! or I should even calculate them?
> See my previous email... the most reliable way is to invoke cpp on your
> .top file to do all the #includes, and then to go through it with a text
> editor and zero out everything that you feel should be zeroed out.
> You'll probably have to halve all of the non-bonded terms yourself by
> hand after the mdrun -rerun.
> > I can't also find what SR and LR and 14 mean in energy terms...!
> short range, long range and 1-4 interactions. See early chapters of
> GROMACS manual for details.
> Mark
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Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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