Re: Fwd: FEP protein-ligand tutorial 2017 unclear section

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 04 2018 - 17:04:28 CDT

I think you are going about this the wrong way.

It's not that every broken or missing feature is a punishment: instead,
good academic software is a gift to you. Please understand that.

Giacomo

On Fri, May 4, 2018 at 3:47 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> It seems that the contribution to /\G of restraining the ligand is
> accounted for in the .namd files with both /Alchemy:Bound and
> /Alchemy:Unbound, and therefore with ParseFEP. Am I wrong?
>
> If I am wrong, is any script to extract /\G from the thermodynamic
> integration runs, so as to "add" to the ParseFEP output? Doing that
> manually, and necessarily repeatedly for long simulations is a punishment
> that perhaps I don't deserve.
>
> thanks
> francesco
>
> On Fri, May 4, 2018 at 5:43 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
> wrote:
>
>> The two files are forward and backward runs of what is essentially TI.
>> It’s been a while since I’ve done it, but I believe you can extract
>> dG/dlambda from the log files and then integrate it.
>>
>> Best,
>> JC
>>
>> On May 4, 2018, at 1:39 AM, Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>> Perhaps this question about "FEP protein-ligand tutorial 2017 unclear
>> section" has passed unnoticed. Thanks for paying attention to.
>> fp
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Wed, May 2, 2018 at 9:51 PM
>> Subject: FEP protein-ligand tutorial 2017 unclear section
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>
>>
>> Hello:
>> With reference to the 2017 "Protein:ligand standard binding free
>> energies: A tutorial for alchemical and geometrical transformations" by
>> Gumbart, Roux, Chipot,it is not clear to me how to deal with the two
>> sections of the archive files
>>
>> 1) Restraints:Bound
>> 2) Restraints:Unbound
>>
>> in the frame of files provided in
>>
>> 3) Alchemy:Bound
>> 4) Alchemy:Unbound
>>
>> i.e, how the contribution of restraints in 1) and 2) is evaluated (in
>> particular, why rest-01 and rest-02?) and algebraically added, if at all,
>> to 3) and 4).
>>
>> I could try to imagine what I am unable to find described in tutorial pdf
>> (otherwise I do not see any README), but a clarification here might avoid
>> taking wrong routes.
>>
>> thanks
>> francesco pietra
>>
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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