Giovanni Mancini wrote:
Dear Gromacs Users,
I am trying to extract the potential of mean force of a small
molecule in a DPPC bilayer. To this end, I applied the methodology
described in an online manual written by Justin Lemkul. My problem is
when I run biasing simulations of the molecule near the interface
(DPPC/water), some lipid molecules move to the water phase. This has as
a consequence a local disorder of the bilayer. Below is the parameters I
employ for the pull code:
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = DPPC
pull_group1 = DTC
pull_rate1 = 0.0
pull_k1 = 1000
Is the position restraints on DPPC molecules a solution to my problem?
It's certainly the most immediate solution that comes to my mind. Try it and
see if it alleviates your issue.
-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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