[gmx-users] afm pulling

[Maik Goette]

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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