Re: Calculation of Diffusion coefficient

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jan 29 2018 - 11:13:55 CST

Thanks, I will work on it.
On 29 Jan 2018 10:14 p.m., "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com>
wrote:

>
>
> On Mon, Jan 29, 2018 at 11:35 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
> wrote:
>
>> Okay, I get that calculating diffusion coefficient may not be of much use
>> in this context.
>>
>> Sorry, I didn't get what you meant by this: "How about you simply take
>> the last part of the ABF simulation, where the biasing force doesn't change
>> much due to convergence, and you assume a net total force of zero on the
>> variable? "
>>
>
> That's for estimating the diffusion coefficient.
>
>
>>
>> If the PMF is converged, then certainly the net total force would be zero
>> on my specified variable. Sorry, I didn't check the convergence till now
>> which I can definitely do by plotting the PMF at the different time point
>> and see whether it is converged or not.
>>
>
> I'd recommend doing that: permeation of a whole peptide across a bilayer
> is a difficult computation.
>
>
>> But if I wanna check the uncertainty of the calculated PMF, I need to
>> have the system force trajectory file for the calculation of say, mean
>> autocorrelation of force at the different regime of the RC [ J. Phys.
>> Chem. B, 2015, 119 (3), pp 1129–1151 ]. So, is there any way I can get
>> that now without re-running all the windows?
>>
>
> For estimating the uncertainty of the PMF (unrelated to the diffusion
> coefficient), try recomputing forces, Colvars and ABF on the existing DCD
> files through "coorfile" and "run 0". If the result is not acceptable to
> you, you may have to run additional trajectories, starting from the latest
> restarts.
>
> Giacomo
>
>
>>
>> Please excuse me being naive about all the intricacies.
>>
>> Thanks for your quick response.
>>
>> On Mon, Jan 29, 2018 at 9:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
>> > wrote:
>>
>>> Hi Souvik, FYI you may also want to take a look at the more recent
>>> papers by Jeff Comer regarding computing permeabilities of small molecules
>>> across a bilayer.
>>>
>>> For something larger, like a peptide, you are definitely much more bound
>>> by the PMF than by the differences in diffusion coefficient. This may be
>>> less of a problem for you, because the diffusion coefficient changes by
>>> less than an order of magnitude between lipid bilayers and bulk water.
>>>
>>> As for recomputing the system force along the trajectory, you do have
>>> its average already computed along the collective variable, given by the
>>> PMF (is it converged?). Computing the system force as a function of time
>>> would only help you in collecting diffusion data during the transient
>>> regime before convergence. Re-running on the single-precision, sparsely
>>> collected trajectories may not be of much help.
>>>
>>> How about you simply take the last part of the ABF simulation, where the
>>> biasing force doesn't change much due to convergence, and you assume a net
>>> total force of zero on the variable?
>>>
>>> Giacomo
>>>
>>>
>>>
>>> On Mon, Jan 29, 2018 at 9:01 AM, Souvik Sinha <souvik.sinha893_at_gmail.com
>>> > wrote:
>>>
>>>> Hi,
>>>>
>>>> Currently, I am estimating a peptide insertion (into membrane) free
>>>> energy profile using ABF. I want to calculate the local diffusion
>>>> coefficient along the reaction coordinate for which I need the estimation
>>>> of 'time autocorrelation function of the fluctuations of the instantaneous
>>>> forces' *[ J. Phys. Chem. B, 2011, 115 (49), pp 14704–14712 ]*--001a11458c320fb78f0563ed5f1e--

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