[gmx-users] Question about COM-Pulling

[Christian Mücksch]

Hi,

although this is not relevant to my previous question:

I used mdrun like this:

mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr 
-g pull.log -px pull_dist.xvg -pf pull_force.xvg

With an input-file like this:

------------------------------------------------
; Run-Parameter
integrator = md
dt = 0.002
nsteps = 1000000

; OUTPUT CONTROL OPTIONS
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000

pull_nstxout = 100 ;
pull_nstfout = 100 ;

rlist = 1.2
ns_type = grid
coulombtype = PME-Switch
rcoulomb = 1.0
vdw-type = shift
rvdw = 1.0
rvdw_switch = 0.9
pbc = xyz

tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 2
ref_p = 1
compressibility = 4.5e-5

DispCorr = EnerPres
continuation = yes

constraint_algorithm = lincs
constraints = all-bonds

pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = reference
pull_group1 = pull
pull_rate1 = 0.01
pull_k1 = 1000
------------------------------------------------

...I get an output for pull_dist.xvg which looks sth. like this:

------------------------------------------------
# This file was created Fri Nov 26 16:22:53 2010
# by the following command:
# /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s 
pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log 
-px pull_dist.xvg -pf pull_force.xvg
#
# mdrun_mpi_4.5.3_s is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "Pull COM"
@ xaxis label "Time (ps)"
@ yaxis label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000 1.1675 3.47701
0.2000 1.1675 3.48043
0.4000 1.1675 3.4795
0.6000 1.1675 3.48214
0.8000 1.1675 3.4869

and so on
------------------------------------------------

In this pull_dist.xvg there is no position of a "dummy"-particle that is 
connected via a harmonic potential to the pull group (as described in 
Grubmüller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding: 
Molecular Mechanics Calculation of the Streptavidin–Biotin Rupture 
Force. In: Science 271 (1996))

In older version of Gromacs I believe that this was the case. Has the 
method changed? How is the force calculated if not by the displacment of the
"dummy"-particle. I just wanted to know how the afm pulling in gromacs 
is achieved without having to look in the source-code.

Thx,
Christian


---------------------------------------------------------------------------------------
Dear Christian:

As per my original comments, please provide a .mdp file, sample
output, and all the other things that I asked for.

Chris.

--original message--

this is a more general question.

I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
at a certain distance from the center of mass of the pull group (compare
figure 6.1 in the manual).
The force is then calculated as the displacement between the pulled atom
and the
"dummy"-particle. So if this is true which I'm not sure of,
I was wondering why the position of this "dummy"-particle is not plotted.

Or does this umbrella pulling work in a different way? How is the force
calculated?

Thanks a lot,
Christian

----------------------------------------------------------------------
The position of the reference group and the displacement of the pulled
group from the reference group should be printed (although perhaps
without the reference position if you are using absolute coordinate
pulling, which is not recommended anyhow).

If you want some better advice, please be more specific and include
cut and paste sections saying "I expected X at Y, but it was not in
the file Z.xvg". you should also include your pull-code .mdp options
and your grompp and mdrun commands.

Chris.

-- original message --

Dear users,

I've got a short question regarding com-pulling. From what I understand
Umbrella pulling is the same as AFM pulling using a harmonic potential.

Why is the position of the spring in the pullx.xvg not printed? One can
only find the vector between both pull groups. I looked into older
Gromacs manuals and in versions < 4 it seems as if this data is printed
to the pullx.xvg file or something similar.

With kind regards,
Christian


-- 
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Email: muecksch at rhrk.uni-kl.de