[gmx-users] AFM pull:don't understand output file (maybe...)

Mario Orsi kurtz219 at yahoo.it
Fri Apr 2 16:36:02 CEST 2004

Hi there,
I'm using the gmx AFM pulling calculations on a
protein with the purpose to stretch it, pulling apart
the two terminal atoms of the backbone. However, in
order to start the simulation with zero force on the
pulled-group I set the .ppa parameter so that I got
this kind of output:

# AFM   3.0
# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'a_1'
# Nr. of pull groups 1
# Group 1 'a_2587'  afmVec 0.000000 0.000000 1.000000 
AfmRate 0.050000  AfmK 2500.000000
0.000000        43.159626    56.754002    56.754002
0.002000        43.160980    56.753578    56.755456
0.004000        43.162025    56.753242    56.756601
I assume that the second-third-fourth columns are the
absolute coordinates of Nend(ref group)-Cend(pulled
group)-Spring positions(more precisely this should be
the position of the spring terminal on which the
pulling force is applied, being the other terminal
attached to the pulled group), respectively.
Hence, taking care that the initial elongation is zero
(i.e. the last two numbers are equal), there should be
no initial force on the pulled group. After the
running, I expect that the spring position coordinate
will be greater than the pulled group position coord:
and this is what I get, actually. The point is that
after reading the gmx manual I'm not so sure I've
understand properly the whole thing... The manual 3.2

"AFM 10.5 3.5 3.63 3.6 The output file consists of the
time, the position of the reference group, and the
position of the pulled group, and the position of the
spring. The position of the pulled group and spring
are in absolute coordinates. Subtract the reference
coordinate to get the position relative to the pulled
group. Note that only the dimensions for which pulldim
is Y are output."

Shouldn't it be "Subtract the reference coordinate to
get the position relative to the REFERENCE group."?

And what about the values? If there is a pulling, how
come the pulled group position has a greater value
than the spring (3.63>3.6)?

Here's my .ppa file:

verbose            = yes
runtype            = afm
group_1            = a_2587
reference_group    = a_1
reftype            = com
pull_dim            = N N Y

afm_rate1                = 0.05 ;nm/ps
; Force constants in kJ/(mol*nm^2)
afm_k1                   = 2500
; Directions
afm_dir1                 = 0.0 0.0 1.0
afm_init1                = 0.0 0.0 13.594376

That was a pretty verbose mail, thanks for your

mario orsi - molecular mechanics research group
politecnico di milano 

"I've got a bad liver, and a broken heart" -T.Waits

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