[gmx-users] afm pulling

Marta Murcia mam2070 at med.cornell.edu
Thu Apr 27 01:32:52 CEST 2006

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

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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