From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jun 23 2017 - 10:00:36 CDT
Check the doc here:
http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html#x1-40002.1
A typical workflow is:
for { set fr 0 } { $fr < [molinfo top get numframes] } { incr fr } {
cv frame $fr
cv frame update
cv printframe
}
On Fri, Jun 23, 2017 at 10:55 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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
>>
>
>
-- 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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