[gmx-users] afm pulling and comm_mode

[Marta Murcia]

Hi again,
I pretty much went about the setting up of afm pulling calculations. 
Still I am a little bit concern about the results. When using gmx3.2.1 
and applying a Linear removal of the center of mass (i.e. translation) I 
see the cell unit still moving during the simulation in a direction 
that, looks to me, is opposite to the force I am applying. In fact, when 
the pulling rate is smaller, the move is not as dramatic. What am I 
doing wrong? I have no note that with 3.3 this doesn't happen. Did 
anyone experience something like that?
Any tip/suggestion will be greatly appreciated
Best
M

Marta Murcia wrote:

> Thanks Emily and Maik for your feed-back
> You both are right regarding the init vector. I happened to be the 
> sign of it as Emily guessed. Changing the direction by doing 
> xpull-xref, ypull -yref, zpull-zref  and not xref-xpull.....works 
> fine.  Thanks for the offer on the script though.
> Thanks Emily for claryfing my confusion on the directional vector
> All the best
> M
>
> Maik Goette wrote:
>
>> Hi
>>
>> There seems to be something wrong with your init-vector.
>> Ich have written a small python script, which simply calculates the 
>> vector for convenience purposes. You still need the pull- and 
>> COM-group coordinates, though. But that shouldn't be a problem.
>> If you want it, I'll send it via mail.
>>
>> Regards
>>
>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> Germany
>> Tel.  : ++49 551 201 2310
>> Fax   : ++49 551 201 2302
>> Email : mgoette[at]mpi-bpc.mpg.de
>>         mgoette2[at]gwdg.de
>> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>>
>>
>> Marta Murcia wrote:
>>
>>> Emily,
>>> I just saw your answer
>>> Thanks a lot
>>>
>>> I just have another question about the unit vector describing the 
>>> direction of pulling. Should it be always a unit vector (1 1 1 for 
>>> example)? Should I asumme then that the direction of the pulling is 
>>> the one specified by the init vector or could I used that same 
>>> vector for example as afm_dir?
>>>
>>> Also, I don't know if I am doing something wrong but using afm_ini 1 
>>> 1 1 and afm_dir as the vector that connects the two atoms I've 
>>> chosen (the pulled and the ref) I am not able to get the spring and 
>>> the pulled atom at the same coordinates at the beginning of pull.pdo 
>>> file.
>>>
>>> # AFM   3.0
>>> # Component selection: 1 1 1
>>> # nSkip 1
>>> # Ref. Group 'm'
>>> # Nr. of pull groups 1
>>> # Group 1 'a_13586'  afmVec 1.000000 1.000000 1.000000  AfmRate 
>>> 0.020000  AfmK 3000.000000
>>> #####
>>>
>>> 0.000000        3.713000        5.627000        5.181000        
>>> 3.694000        3.732000        5.712000        5.542000        
>>> 4.890000        5.472001
>>>
>>> I was able to get it, though, using absolute coordinates leaving the 
>>> reference group blanck (using gromac 3.3 since in 3.2.1 there is a 
>>> bug on absolute coordinates)
>>>
>>> #AFM   3.0
>>> # Component selection: 1 1 1
>>> # nSkip 1
>>> # Ref. Group ''
>>> # Nr. of pull groups 1
>>> # Group 1 'a_13586'  afmVec 1.000000 1.000000 1.000000  AfmRate 
>>> 0.020000  AfmK 3000.000000
>>> #####
>>> 0.000000      0.000000        0.000000        0.000000        
>>> 3.694000        3.694000        5.712000        5.712000        
>>> 4.890000        4.890000
>>>
>>>
>>> what is wrong? am i choosing the wrong starting vector when using a 
>>> reference group? (Note that I am using  xref-xpull, yref-ypull, 
>>> zref-zpull  as afm-ini, 0.019 -0.085 0.291)
>>>
>>> Again, thanks a lot
>>> M
>>>
>>> Emily Walton wrote:
>>>
>>>> Hi,
>>>>
>>>>> Dear all,
>>>>> I am simulating an unbinding process with the pull code (afm option).
>>>>> I've been reading previous posts about this option and I just  
>>>>> wanted to
>>>>> clarify some ideas and ask some questions. There are:
>>>>> 1-The pulling can be done choosing two different molecules. Why a
>>>>> particular group within a molecule can not be used? Not even as a
>>>>> reference group?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Any group that is defined in your index file (specified with mdrun 
>>>> - pn pull.ndx) can be used. Look at made_ndx in the manual to learn 
>>>> how  to add new groups.
>>>>
>>>>> 2-Should I need to fixed the center of mass of the protein to avoid
>>>>> shifts? How can I do that? Would it be OK to use posre for the  
>>>>> backbone
>>>>> of the protein with carrying out the pulling?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> It depends on what you want to do. Typically, something would need 
>>>> to  be fixed. In ligand-protein systems, the center of mass of the  
>>>> protein is a reasonable choice. It was used by Grubmuller et al. 
>>>> in  their 1996 Science paper on the unbinding of 
>>>> biotin-streptavidin.  (Science, 271:954–5, 1996) For unraveling of 
>>>> proteins, one terminal  atom may be fixed while the other is pulled.
>>>>
>>>> Fixing the center of mass of a group in the index file can be done 
>>>> in  the .mdp file you feed to grompp. See the manual, chapter 7.
>>>>
>>>>> 3-Should I removed all the constraints for the bonds (SHAKE, lincs)?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I think this is a matter of preference. Some people do, some 
>>>> people  don't. Again, it will depend on your system- is it stable 
>>>> without the  constraints?
>>>>
>>>> The bonds that are broken with afm pulling are bonds described by 
>>>> non- bonded interaction terms in gromacs. These bonds wouldn't be  
>>>> constrained by shake or lincs anyway, so the presence or absence 
>>>> of  constrains should have a minimal effect on the simulation results.
>>>>
>>>>> 4-once I have the pull.pdo the calculation of the applied force  
>>>>> will be
>>>>> F= K*(zspring -zgroup) (assuming I am pulling in the z direction)?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Yes. The spring is an ideal spring, so force is k*(extension). The  
>>>> extension can be calculated from the pull.pdo file.
>>>>
>>>>
>>>> -Emily Walton_______________________________________________
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>>>
>>>
>>>
>>>
>>>
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>
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