[gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

Vedat Durmaz durmaz at zib.de
Thu Oct 20 10:25:54 CEST 2011

thanks mark. i guess it took some time answering all these questions. 
and i think you are right. trying to interpret each computed energy term 
seperately in a physical manner is senseless. especially since i'm not 
really deep inside the force field & implementation stuff. however, with 
one of your statements i cannot agree at all:

imho, free energy diff's on the basis of two conformations and their 
steady state distribution are independent from both the energy and type 
of the intermediate state. it's only the conversion's rate that does 
depend on it.

but the reason, why i refrained from extracting the potential energy for 
a subset of my system was simply due to the difficulties to find 
"detailed information" about how to play it out although many gromacs 
users have been asking for the issue over the last years. i needed 
nearly one full day to figure it out even though it's a simple series of 
about 4 gromacs commands only, given some md input & result files like 
md.xtc, md.gro, complex.top, index.ndx:

|grompp -f mdSubset.mdp -c md.gro -p complex.top -o mdSubsetTemp.tpr|
|echo ||"1"| || tpbconv -s mdSubsetTemp.tpr -nsteps ||0| |-n index.ndx 
-o mdSubset.tpr|
|echo ||"1"| || trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc|
|mdrun -s mdSubset.tpr -rerun mdSubset.xtc -v -deffnm mdSubset|

where "1" stands for the group to be extracted (from the list of groups 
in the index file) and "-nsteps 0" causes recomputation of for the 
extracted subset at the given time steps only. i mention it here so that 
other users looking for the details might find them a little bit faster 
... it's especially this kind of "tiny tutorials" that i miss e. g. on 
the gromacs website.

thanks for listening and kind regards,


>> Q8 does anyone have an idea, how to perform the simulation and on 
>> which energy terms to concentrate in order to get reliable results?
> You seem to be performing it OK, given that you've said very little 
> about any details...
> I think the problem is poorly constructed. You have some experimental 
> data that gives a general understanding of the size of the free energy 
> difference between the isomers. You can't necessarily expect to 
> reproduce that from (average) potential energy differences between 
> conformations of those isomers. Measuring the free energy difference 
> with simulations is hard because you cannot model the intermediate 
> stages of bond breaking and forming. There are "alchemical" free 
> energy methods that could in principle treat this problem effectively, 
> but there will be some significant issues and you are best doing your 
> own homework there.
> Mark
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