From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jun 24 2017 - 01:22:17 CDT
In other words, are 1.889e+01, 5.2e+01, -3.396e+01, 9.26e+00, 1.01e+02, and
-5.05e+01 pertaining to r, Theta, Phi, Psi, theta and phi , in the order?
Certainly not to "r", which was directly measured as 27.6.
thanks
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Jun 23, 2017 at 7:06 PM
Subject: Re: namd-l: measuring Euler angles and polar angles
To: Jérôme Hénin <jerome.henin_at_ibpc.fr>
Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>, Giacomo Fiorin <
giacomo.fiorin_at_gmail.com>
Hi Jerome:
Thanks. However, how to use the other "numbers" to update the colvars file
in order to carry out ABF with my system? I have already selected the
groups of atoms of the protein and the ligand, and measured the distance
between the center of mass of the protein and the ligand. What is missing
are updated Euler and polar angles.
thanks
francesco
On Fri, Jun 23, 2017 at 5:04 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Francesco,
>
> The files with a lot of zeroes are written because your input defines an
> ABF bias, but of course ABF has nothing special to do if you're just
> analyzing a trajectory and not running a simulation. So you could delete
> the ABF entry from the input, or if you want to keep using the same input,
> you can safely ignore those ABF output files.
>
> Jerome
>
> On 23 June 2017 at 16:55, 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
>>>
>>
>>
>
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