Re: increment torsion restrain before minimization

From: Tina Stokelj (tinastokelj_at_gmail.com)
Date: Mon Nov 05 2012 - 07:16:59 CST

Hi Norman,

I was wondering, if I construct a separate .cfg and extrabondsfile for any
of 361 minimizations.... The next question is: How do I run multiple .cfg
files in command line?

*Best regards, *
*Tina Stokelj*
*PhD at University of Trieste*

On Mon, Nov 5, 2012 at 1:38 PM, Tina Stokelj <tinastokelj_at_gmail.com> wrote:

> *Thank you Norman, *
> **
> *it was a godd idea, I didn't thought about it. I included suggested in
> .cfg file, but NAMD only ran the first simulation, with extrabonds file1.
> Then an eroor occurs:*
> **
> *TCL: Setting parameter extrabondsFile to extrabonds2.txt*
> *FATAL ERROR: Setting parameter extrabondsFile from script failed!*
> **
> *I also tried to copy entire script in the .cfg. file twice. As before
> the first minimization runs normally, but for the second script the error
> occurs:*
> **
> *FATAL ERROR: setting parameter coordinates from script failed
> (Reading coordinates from .pdb file is the first action called in script.)
> *
> **
> *I append the content of my extrabonds.txt file:*
> **
>
> #Add torsional angle restrain
> # dihedral a1 a2 a3 a4 kref
> dihedral 1 2 24 28 1. 20.
> dihedral 7 1 2 24 1. 180.
>
>
> *And the content of my configuration file:*
>
>
> # NAMD Config file - autogenerated by NAMDgui plugin
> # Author: Jan Saam, saam_at_charite.de
> # input
> coordinates tina_solvated.pdb
> structure tina_solvated.psf
> parameters par_all36_sugar_tip3.inp
> paratypecharmm on
> # output
> set output minimization
> outputname $output
> dcdfile ${output}.dcd
> xstFile ${output}.xst
> dcdfreq 50
> xstFreq 50
> binaryoutput no
> binaryrestart no
> outputEnergies 100
> restartfreq 1000
> fixedAtoms off
> # Basic dynamics
> exclude scaled1-4
> 1-4scaling 1
> COMmotion no
> dielectric 1.0
> # Simulation space partitioning
> switching on
> switchdist 10
> cutoff 12
> pairlistdist 14
> # Multiple timestepping
> firsttimestep 0
> timestep 1
> stepspercycle 10
> nonbondedFreq 1
> fullElectFrequency 2
> # Temperature control
> set temperature 298
> temperature $temperature; # initial temperature
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
> extraBonds yes
> extraBondsFile extrabonds.txt
>
> # Scripting
> minimize 3000
>
> *Maybe there is still some other way to do it? *
> **
> *Best regards, *
> *Tina Stokelj*
> *PhD at University of Trieste*
>
> On Mon, Nov 5, 2012 at 8:32 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> 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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