Re: increment torsion restrain before minimization

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Nov 05 2012 - 07:35:19 CST

Hi,

Perhaps the colvars
module<http://www.ks.uiuc.edu/Research/namd/2.9/ug/node53.html>of NAMD
would be helpful for you? It's easy to restrain the torsions using
the dihedral colvar. You can easily get the free energy map using
metadynamics or ABF.

What do you mean by "*calculate free energy after minimization*"? After
minimization you can only get the energy. For the entropy contributions to
the free energy you need to run some more sampling simulations.

Best regards,
Ajasja Ljubetič

On 3 November 2012 15:59, Tina Stokelj <tinastokelj_at_gmail.com> wrote:

> *Hi,*
> **
> *my name is Tina Štokelj, I am a new NAMD user.*
> *I want to investigate the conformational space of dissacharide based on
> molecular mechanics simulation. To get an adiabatic conformational map I
> need to:*
> *1.) restrain two torsion angles psi and phi in the dissacharide
> molecular structure, with many combinations (I plan to make a map with grid
> 19X19)*
> *2.) calculate free energy after minimization *
> **
> *The torsion angles in NAMD may be restrained with Extrabonds file, but I
> have to change the values of torsional angles before I run any of the 361
> minimizations!*
> *It would be nice to cobine torsion restraint with a loop including incr,
> such as for example in Tk Console. Keeping one dihedral at the value -180
> and increment second dihedral in interval [-180, 180]*
>
>
> >Main< (cellobiosemin) 71 % set dihed1_atoms {
> set one [atomid CARB 1 C4]
> set two [atomid CARB 1 O4]
> set three [atomid CARB 2 C1]
> set four [atomid CARB 2 O5]
> }
>
> set one [atomid CARB 1 C4]
> set two [atomid CARB 1 O4]
> set three [atomid CARB 2 C1]
> set four [atomid CARB 2 O5]
>
> >Main< (cellobiosemin) 72 % set init_dihed1 -180
> -180
> >Main< (cellobiosemin) 73 % set dihed2_atoms {
> set one [atomid CARB 1 C5]
> set two [atomid CARB 1 C4]
> set three [atomid CARB 1 O4]
> set four [atomid CARB 2 C1]
> }
>
> set one [atomid CARB 1 C5]
> set two [atomid CARB 1 C4]
> set three [atomid CARB 1 O4]
> set four [atomid CARB 2 C1]
>
> >Main< (cellobiosemin) 74 % set init_dihed2 -180
> -180
> >Main< (cellobiosemin) 75 % for {set init_dihed1 -180; set init_dihed2
> -180} {$init_dihed2 < 181} {incr init_dihed1 0; incr init_dihed2 20} {
> puts "dihed1: $init_dihed1"
> puts "dihed2: $init_dihed2"
> }
> dihed1: -180
> dihed2: -180
> dihed1: -180
> dihed2: -160
> dihed1: -180
> dihed2: -140
> dihed1: -180
> dihed2: -120
> dihed1: -180
> dihed2: -100
> dihed1: -180
> dihed2: -80
> dihed1: -180
> dihed2: -60
> dihed1: -180
> dihed2: -40
> dihed1: -180
> dihed2: -20
> dihed1: -180
> dihed2: 0
> dihed1: -180
> dihed2: 20
> dihed1: -180
> dihed2: 40
> dihed1: -180
> dihed2: 60
> dihed1: -180
> dihed2: 80
> dihed1: -180
> dihed2: 100
> dihed1: -180
> dihed2: 120
> dihed1: -180
> dihed2: 140
> dihed1: -180
> dihed2: 160
> dihed1: -180
> dihed2: 180
> >Main< (cellobiosemin) 76 %
>
>
>
> Is it possible to increment torsion restrains with loop in Extrabonds or
> configuration file before next minimization starts automatically? Is there
> any other solution to overcome this problem?
>
> Best regards,
> Tina Štokelj
> Phd student at University of Trieste
>
>
>
>
>

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