From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Mon Jun 22 2020 - 02:22:06 CDT
you do not need to modify your *alchFile* file multiple times. Just set
the *alchCol* to the value of your choice (1 for appearing atoms, or -1
for vanishing ones). The parameters that you will use with the fep.tcl
script (which set *alchLambda* and *alchLambda2*) will determine whether
you will carry out a creation or an annihilation in your forward or
backward run. For instance, let us assume that you assign a 1 to the
five atoms of methane in your *alchFile* file, and declare in your NAMD
config file: runFEP 0.0 1.0 0.01 $*numSteps* (forward run). NAMD will
grow methane and the final free energy will be the net solvation free
energy. Conversely, if you declare in your NAMD config file: runFEP 1.0
0.0 -0.01 $*numSteps* (backward run), NAMD will shrink methane, and the
final free energy will be the negative of the solvation free energy.
Alternatively, you could have assigned -1 to the five atoms of methane
in your *alchFile* file, in which case declaring runFEP 1.0 0.0 -0.01
$*numSteps* would have given you the solvation free energy (and runFEP
1.0 0.0 -0.01 $*numSteps*, its negative).
On 6/22/20 6:32 AM, Qasim Pars wrote:
> 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 <mailto: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:
> I hope this is helpful,
> On Mon, 22 Jun 2020 at 08:34, Qasim Pars <qasimpars_at_gmail.com
> <mailto: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
-- Chris Chipot, Ph.D. CNRS research director, University of Lorraine Adjunct professor of physics, University of Illinois, Urbana-Champaign _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3161 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-4361 E-mail: chipot_at_ks.uiuc.edu Christophe.Chipot_at_Univ-Lorraine.fr Web: http://www.ks.uiuc.edu/~chipot http://www.lia-uiuc.cnrs.fr The light shines in the darkness, and the darkness has not overcome it John 1:5 _______________________________________________________________________
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