AW: increment torsion restrain before minimization

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 05 2012 - 01:32:39 CST

Hi Tina,

 

first of all you should try some seperate extrabonds files, and a script like

 

extrabonds on

extrabondsfile file1

minimize 10

extrabondsfile file2

minimize 10

 

Of course the files should affect the same atoms. If you see this works like expected, you could simply create this extrabondsfiles with the tcl interface between the minimize runs.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Tina Stokelj
Gesendet: Samstag, 3. November 2012 16:00
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: increment torsion restrain before minimization

 

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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