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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