Lin, Dejun wrote:
Thank you Justin. But I'm still confused about the pull_vec1. Is the vector
pointing from the reference or from the pull group for all the geometry
settings? For instance, if I use pull_geometry = position, pull_dim = N N Y,
pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position =
pull_init + time*pull_rate*pull_vec1 according to the manual and it's
actually pulling the pull group away from the reference because the vector
has a positive z component.
The reference group serves as the reference :) Thus, the vector connecting your
reference and pull group is (0,0,1) since the pull group has a larger
z-coordinate. You're right about the position equation, but you've got a
pull_rate1 of zero, so the added term drops out and position = pull_init1.
BTW, I did consider using position geometry but can I get the PMF using
pull_rate NOT equal to zero? The reason I turned to cylinder is that with
"distance" geometry the membrane concaved as the micelle was restrained to a
very short distance (any distance below the critical distance where the
fusion was supposed to occur) without fusing and this would persist for some
hundred nanoseconds.
To obtain the PMF, the pull rate should be zero, using several (many)
independent simulations along the desired reaction coordinate. See the tutorial:
http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
-Justin
Thanks again for your help! Dejun
________________________________________ From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list
for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of
cylinder
Lin, Dejun wrote:
Hi all,
I want to do an umbrella sampling to calculate the potential of mean force
of a micelle fusing to a lipid membrane. In the starting configuration, the
membrane normal is set in z direction and the membrane is under the
micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used
pull_geometry = distance but the sampling took to long to converge. And
then I considered using cylinder instead and set up the pull code as: pull
= umbrella pull_geometry = cylinder pull_dim = N N Y pull_start =
no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle
pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1
= 1.8 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000
pull_nstfout = 1000
And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0.0000
23.3397 4.90267 100.0000 0.742426 1.86002
200.0000 0.737842 1.86232 300.0000
0.762641 1.83985 400.0000 21.6814
1.86777 500.0000 0.771017 1.82482 600.0000
0.789036 1.83254 700.0000 0.793745
1.83503 800.0000 0.804732 1.84217 900.0000
0.80137 1.84166 1000.0000 0.817979 1.83546
1100.0000 0.806272 1.83535 1200.0000 0.792355
1.80372 1300.0000 0.786839 1.8438 1400.0000 0.798686
1.82625 1500.0000 0.802859 1.84138 1600.0000 0.803844
1.84379
(pf.xvg) 100.0000 -480.158 200.0000 -498.547
300.0000 -318.839 400.0000 -542.14 500.0000
-198.526 600.0000 -260.291 700.0000 -280.22
800.0000 -337.385 900.0000 -333.317 1000.0000 -283.644
1100.0000 -282.761 1200.0000 -29.7684 1300.0000 -350.409 1400.0000
-209.991 1500.0000 -331.029 1600.0000 -350.309
And I visualized the trajectory in VMD and found that an "explosion" of the
micelle (with all its residues scattered in the box). I then changed the
pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion"
was gone and everything seemed to work. But I'm not quite sure if I'm
setting up the pull-code right because if z(COM-membrane) < z(COM-micelle),
then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I
think my
The negative is incorrect. If the micelle is "above" the membrane (i.e., it
has a greater z-coordinate), then the reference vector should be positive
with respect to the reference position. It would appear from the pullx.xvg
file that you've got some weird PBC crossing going on, since the reference
positions oscillate dramatically at the beginning of the simulation.
pull-code is restraining the COM of the micelle to the COM of a "cylinder"
of the membrane at a distance of 1.8nm, with the vector pointing from
COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what
caused the explosion or am I setting up the pull-code right? And what are
the 2nd and 3rd column in the px.xvg output in this case?
For such a simple restraint, I don't think there is any need for cylinder
geometry. You're not using different weighting. Any of the other
pull_geometry settings should work, with "distance" probably being the most
intuitive. I suspect it would be very easy to use the "position" setting as
well.
The output in the pullx.xvg file should be labeled in the header. The
generic output is (x,y,z) of the reference group, followed by delta(x,y,z)
for the restrained group, i.e. how far away the restrained group is along
each coordinate axis. If you're only restraining/pulling along the z-axis,
then the only terms written are z and dz, since, in principle, x, y, dx, and
dy are all fixed, with the last two terms being zero.
-Justin
-- ========================================
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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========================================
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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