Tom wrote:
Justin
you have good experience of pulling.
If you have time, please help with this publling problem:
abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!
I already commented:
http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html
i am pulling A object towards B along z-axis. But system
has pbc on x, y and z. Is it because of the pbc image of B
object that make grmx confused to report the sign.
Likely. If your box is not greater than about 16.3 nm in Z, then you'll have
this problem.
In my system, A should be on the top of B in z-axis, but i just noticed
that at the intial step: 1dZ has been negative already.
It seems the system use the PBC image (in z-axis) of the reference object B
to cacluate 1dZ, right?
Sounds right.
-Justin
--------------------------------------
@ 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 0.77622 -8.13474
------------------------------------
Thanks a lot for the help!
Tom
---------- Forwarded message ----------
From: Tom <[email protected]>
Date: Sun, 16 Oct 2011 23:02:09 +0800
Subject: about the pulling
To: gmx-users <[email protected]>
Dear Gromacs Users or Developers,
I am using the pulling the COM of object A towards B using:
---------------------------------
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = B
pull_group1 = A
pull_rate1 = -0.00005714
pull_k1 = 5000
-------------------------------
On the output file of pullx.xvg, the sign of dZ
has been changed from negative to posivitve
or vice vrsa in all sudden. What does it mean?
The following is an example:
@ 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"
---------------------------------------------------
173.7400 0.77622 8.14856
173.7500 0.77622 8.14897
173.7600 0.77622 8.14938
173.7700 0.77622 8.14977
173.7800 0.77622 -8.14987
173.7900 0.77622 -8.14954
173.8000 0.77622 -8.14924
173.8100 0.77622 -8.14895
------------------------------------
Thanks a lot for the information!
Thanks,
Tom
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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