From: Qasim Pars (qasimpars_at_gmail.com)
Date: Sun Jun 21 2020 - 23:32:28 CDT
Thanks. Let's suppose I want to calculate the solvation free energy of
methane which is the first residue in the decouple.fep file. I am a bit
confused now. Which of the following is true?
1-) For the forward state (0->1) I have to change the values in the beta
column to 1 for the 1st residue in the decouple.fep file. And for the
backward state (1->0) I have to change the values in the beta column to -1
for the 1st residue in the decouple.fep file. The beta values of other
residues will be 0 (zero), right?
2) For both the forward and backward state I have to change the values in
the beta column to 1 for the 1st residue in decouple.fep file. The beta
values of other residues will be 0, right?
On Mon, 22 Jun 2020 at 05:26, Michael Robinson <michael.robinson1_at_monash.edu>
> Hi Qasim,
> I would advise looking at the NAMD documentation for running free energy
> calculations, in particular this page on the input files:
> This page should explain most of the questions you may have about the
> unique aspects of the configuration file example you showed above. For
> example, the free energy tutorial's .conf file contains the following lines:
> alchFile decouple.fep
> alchCol B
> These lines state that the decoupled residues are detailed in the file 'decouple.fep' (alchFile), and that the information is stored in the beta column of the file (alchCol). Typically this means any non-0 values in the beta column will select that atom (i.e. to perform the calculation on the 3rd residue, change the values in the beta column to 0 for the 1st residue, and to 1 for the 3rd residue). I would like to emphasise the importance of reading the entire set of information about free energy methods: https://www.ks.uiuc.edu/Research/namd/2.13/ug/node59.html.
> I hope this is helpful,
> On Mon, 22 Jun 2020 at 08:34, Qasim Pars <qasimpars_at_gmail.com> wrote:
>> Dear users,
>> Please look the input file in this free energy tutorial:
>> How does NAMD know which residue to (de)coupled during the hydration free
>> energy calculation? Note that it's the first residue in the tutorial.
>> If I want to decouple the third residue in the psf/pdb for the solvation
>> free energy calculation, what should I do in the input file? ( that is, I
>> want to calculate the solvation free energy of the third residue).
>> Any help will be appreciated.
>> Qasim Pars
-- Qasim Pars
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