From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Mon Sep 12 2016 - 13:34:22 CDT
Brian,
Thank you very much for your reply and the explanations. I will work on
that.
Best regards,
Azadeh
On Mon, Sep 12, 2016 at 10:01 PM, Radak, Brian K <bradak_at_anl.gov> wrote:
> I have not worked with the pair interaction utility, but if the selection
> is done in the B column before the calculation, I doubt that a dynamic
> selection is possible, since those assignments are only done when the
> "structure" command is called.
>
> You might be able to hack this by swapping the coordinates of certain
> water molecules via Tcl in between energy evaluations, but that assumes: 1)
> you can determine which molecules you want on-the-fly (maybe via
> "measure"?) and 2) the number of atoms in the selection is fixed. The
> validity of number 2 probably depends on how you define the first solvation
> shell.
>
> HTH,
> Brian
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Azadeh Alavi [azade.alavi_at_gmail.com]
> *Sent:* Monday, September 12, 2016 6:49 AM
> *To:* NAMD list
> *Subject:* namd-l: PMF decompostion
>
>
> Dear Namd users
>
> I have a membrane-protein system using charmm36 force field and have
> calculated the PMF profile for the permeation of an ion across the channel
> using the ABF method. I wished to know how to decompose the PMF profile
> into individual contributions from the ion’s interactions with its first
> solvation shell water (defined as 3.3 A° from sodium for instance), using
> pair interaction utility in NAMD. As far as I know, in the this utility, a
> file should be prepared in which selected atoms are to be distinguished by
> 1 and 2 in the B column. However, in order to consider the first solvation
> shell water, the file needs to be updated while the .dcd file is being read
> and I do not know how it it is possible.
>
> Your help would be greatly appreciated.
> Thank you.
>
> Best regards,
> Azadeh
>
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