[gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

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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