[gmx-users] afm pulling

Marta Murcia mam2070 at med.cornell.edu
Tue May 2 15:37:06 CEST 2006


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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