Re: Total energy of a residue

From: Mert Gür (gurmert_at_gmail.com)
Date: Tue Jun 23 2009 - 14:59:19 CDT

It worked. Thanks a lot.
Best,
Mert

On Tue, Jun 23, 2009 at 7:03 PM, Brian R Novak <bnovak1_at_lsu.edu> wrote:

> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu on behalf of Mert Gür
> Sent: Tue 6/23/2009 10:08 AM
> To: NAMD list
> Subject: namd-l: Total energy of a residue
>
> Dear all,
> I want to evaluate the internal energy of a residue and the interaction
> energy of this residue with the other residues in one step. Would it make
> sense to define just the second selection as the whole protein so that I
> will end up with the sum of the two mentioned energies.
>
>
> set sel1 [atomselect top "residue 2"]
> set sel2 [atomselect top protein]
>
> namdenergy -ofile "pe.dat" -all -sel $sel1 $sel2 -par
> ./common/par_all27_prot_lipid.inp
>
> In case it does not make any sense, I need to define the second selection
> to
> be the whole protein except the selected residue. So that I can evaluate
> the
> energies separately.
> How can I do that without writing each residue index separately into the
> parenthesis in the second selection?
>
> set sel1 [atomselect top "residue 2"]
> set sel2 [atomselect top "whole protein , residue2 excluded"]
>
> I think "protein and not residue 2" should work for sel2
>
> namdenergy -ofile "pe.dat" -all -sel $sel1 $sel2 -par
> ./common/par_all27_prot_lipid.inp
>
> Best,
> Mert
>
>
>
>
> NAMDEnergy operates on either one or two selections; if only one selection
> is chosen, then internal energies for that selection will be calculated,
> whereas if two selections are chosen, only interaction energies between
> those selections will be calculated. Selections are given using the
> standard
> VMD atom selection language.
>
>
>
> Brian Novak
> Postdoctoral Researcher
> Mechanical Engineering
> Louisiana State University
> (225)578-0301
>

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