On 20/10/2011 7:25 PM, Vedat Durmaz wrote:
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.
I'm not sure with which statement of mine you are disagreeing. The free
energy is a state function, and so the free energy difference between E
and Z isomers does not depend on the path taken for the conversion. The
difficulty is just that there is no path for a cyclic alkane from E to Z
in a normal MD force field.
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.
There's an art to trying to find detailed help. I know I've given the
advice to make subsets and use mdrun -rerun several times, but I don't
know how a newcomer is ever going to figure that out on their own!
BTW -nsteps 0 is not necessary. mdrun -rerun only computes on the frames
present in the input trajectory file. Also, if the index group of
interest is already present in the .tpr that ran the simulation, then
you can do the job with variations on only the latter three commands.
Mark
thanks for listening and kind regards,
vedat
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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