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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists