On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse
transformation onto that of forward with both axes reversed. so i
should expect overlap. this is consistent with whatever you are saying. i
am sorry for negligence and confusion.
And taking the negative?
yes
but when i use SC while coulomb transforamtion also, as in LJ
transformation, the curves overlap. Now the question is why is it
necessary to use SC during charge transformation to get overlap of the
curves. It makes no sense at least to me.
My experience has been that when you turn on soft core, you get a
lambda-dependent shape of the dG/dlambda curve *regardless* of what
transformation you're doing (i.e., even if you're doing NOTHING).
i too see the dependence.
I don't understand what do you mean by "doing NOTHING". Do you mean that
initial and final states are the same, so the net change is NOTHING?
Yes, when making no change to a molecule, there's still a lambda
dependence with soft core. I assume this has to do with details of the
implementation. It's only the TOTAL free energy change that is zero.
Since both of your transformations here are small, with soft core on,
your curve shape will be dominated by that characteristic shape from
soft core, and so it will *appear* that your curves overlap perfectly.
i have no experience of large transformations, but, i think, even there
also the characteristic shape would be observed. anyway, only difference
potentials are contributing and non-bonded interactions, which are
getting soft-cored, will be too many than bonded ones (if you perturb
bonded-interactions also). May be i am wrong, as bonded interactions are
much stronger than nonbonded which would cancel the nonbonded
contributions.
My point is just that if you're trying to see "signal" (lambda
dependence that is not due to soft core) buried in "noise" (the
characteristic soft core shape of the curve) the "signal" has to be
significant.
Now, the modified question: why is there no overlap of the graph in the
absence of SC potentials for charge transformations (again when plotted on
the reverse scales, both x and y)?? The overall mod(dG) is also not same
for both the simulations.
I am not sure whether it is because of undersampling.. i don't think so.
I am clueless.
What exactly do you mean by "no overlap"? i.e., if you compute the two
DeltaG values, how different is DeltaG_forward from -DeltaG_reverse?
How does the difference compare to your computed uncertainty? All I
can tell you at this point is that, if you are doing enough sampling,
you have everything set up properly, and there are no bugs,
DeltaG_forward MUST be equal to -DeltaG_reverse (within error).
The amount of help we can provide is directly related to how much
information you give; when you just say they don't overlap, it's hard
to do anything to help. You could try providing us with <dG/dl> values
at each lambad, or even with your topologies and run scripts so I can
reproduce what you're doing....
i have sent the files to you off-list.. plz have a look at.
thanks
bharat
David
bharat
please help.
bharat
You need to provide more detail on your protocol.
David
i tried this for simple ala->gly and ethane->methane transformations.
please give me some insight into the problem...
bharat
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