Re: measuring Euler angles and polar angles

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 23 2017 - 09:55:31 CDT

Hi Giacomo
Thanks for your input. I bag pardon for my naive status here. Could you
please have a look at the outputs from cv below? (the input .in file was
the original one from protein-ligand tutorial, i.e., r =21.5, not the
actual 27.6 pertaining to my system). I am confused as to what I could use
to update the values in my previous mail.

Thanks a lot for your understanding

francesco
Loading 5xxf_SAA1_box_ion.psf
npt-09_58.2ns.pdb

tk console

loading history file ... 24 events added
Main console display active (Tcl8.5.6 / Tk8.5.6)
(Conformation:5xxf-SAA1) 25 % cv molid 0
>Main< (Conformation:5xxf-SAA1) 26 % cv configfile bound-1.in
>Main< (Conformation:5xxf-SAA1) 27 % cv update

whereby 6 hidden files are printed in the work directory

.count

# 1
# 0.3 0.05 14 0

 0.325 0
 0.375 0
 0.425 0
 0.475 0
 0.525 0
 0.575 0
 0.625 0
 0.675 0
 0.725 0
 0.775 0
 0.825 0
 0.875 0
 0.925 0
 0.975 0
_________________________

.zar.grad

# 1
# 0.3 0.05 14 0

 0.325 0
 0.375 0
 0.425 0
 0.475 0
 0.525 0
 0.575 0
 0.625 0
 0.675 0
 0.725 0
 0.775 0
 0.825 0
 0.875 0
 0.925 0
 0.975 0
_____________________

.czar.pmf

       xi A(xi)
       0.3 0
      0.35 0
       0.4 0
      0.45 0
       0.5 0
      0.55 0
       0.6 0
      0.65 0
       0.7 0
      0.75 0
       0.8 0
      0.85 0
       0.9 0
      0.95 0
         1 0
____________________________________

.grad

# 1
# 0.3 0.05 14 0

 0.325 0
 0.375 0
 0.425 0
 0.475 0
 0.525 0
 0.575 0
 0.625 0
 0.675 0
 0.725 0
 0.775 0
 0.825 0
 0.875 0
 0.925 0
 0.975 0
______________________
.pmf

# xi A(xi)
       0.3 0
      0.35 0
       0.4 0
      0.45 0
       0.5 0
      0.55 0
       0.6 0
      0.65 0
       0.7 0
      0.75 0
       0.8 0
      0.85 0
       0.9 0
      0.95 0
         1 0
___________________________

.zcount

# 1
# 0.3 0.05 14 0

 0.325 0
 0.375 0
 0.425 0
 0.475 0
 0.525 0
 0.575 0
 0.625 0
 0.675 0
 0.725 0
 0.775 0
 0.825 0
 0.875 0
 0.925 0
 0.975 0
_______________________

>Main< (Conformation:5xxf-SAA1) 28 % cv printframe
           0 1.88926419197828e+01 5.22845307973583e+01
-3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
-5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00

>Main< (Conformation:5xxf-SAA1) 29 %

On Thu, Jun 22, 2017 at 7:18 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Francesco, fire up the Colvars module in VMD and load the same variable
> definition used in the tutorial. You can use the "cv" command (examples:
> "cv update" and "cv printframe") to get the numbers.
>
> Giacomo
>
> On Thu, Jun 22, 2017 at 1:01 PM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hi:
>> While r between centers of mass is OK, I would appreciate being directed
>> to vmd commands for getting Euler and polar angle equilibrium values in
>> connection with protein-ligand ABF beyond the tutorial
>> thanks
>> francesco pietra
>>
>>
>> #############################################################
>> # RESTRAINTS AND PMF
>> #############################################################
>>
>>
>> harmonic {
>> colvars r
>> forceConstant 0.0
>> centers 27.6 # OK measured
>> }
>>
>>
>> harmonic {
>> colvars Theta
>> forceConstant 0.0
>> centers 97.8
>> }
>>
>>
>> harmonic {
>> colvars Phi
>> forceConstant 0.0
>> centers -9.2
>> }
>>
>>
>> harmonic {
>> colvars Psi
>> forceConstant 0.0
>> centers 22.9
>> }
>>
>>
>> harmonic {
>> colvars theta
>> forceConstant 0.0
>> centers 40.8
>> }
>>
>>
>> harmonic {
>> colvars phi
>> forceConstant 0.0
>> centers -78.2
>> }
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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