WU Yanbin wrote:
Dear GMXers,
I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is
placed at various locations of a channel to compute the energy barrier
of the entrance.
Below is the PMF section of mdp input, to compute the PMF around the
position of (4.04700, 4.0582, -2.2058). The pulling molecule is
initially placed close to the (4.04700, 4.0582, -2.2058) position.
The box size is 8.094*8.1164*6.0. The series of positions I considered
is in the z-coordinate range of -2.2 to -0.8.
-----------------------
pull = umbrella
pull_geometry = position
pull_dim = N N Y
pull_start = no
pull_ngroups = 1
pull_group0 =
pull_group1 = MOL1
pull_init1 = 4.04700 4.05820 -2.2058
pull_rate1 = 0.00
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000
-----------------------
For this particular configuration, should I use "pull-geometry=position"
or "pull-geometry=distance"? Or they are the same for this case?
I read the manual and PMF tutorial but cannot figure this out. Could
anyone provide more details about this?
The "distance" method won't work. Have you seen the following:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html
To pull something through a channel, either "position" or "direction" should be
able to do it.
-Justin
Thank you.
Best,
Yanbin
--
========================================
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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