Shilpi Chaurasia wrote:
I am trying to pull apart two dimers of tubulin protein joined
together, to form two separate dimers by steered molecular dynamics
using Pull code. The objective is to separate the dimers by pulling
along one axis only (Y axis). I ran the simulation for 25 ps and it
accomplished well but while visualizing the trajectory in VMD, in the
very beginning (first frame), dimers are at distance which is much
greater than expected. I expected that in first frame they should not
have separated too much (i.e. in just 1 ps, they are at greater
distance) I guess this is unusual. Please let me know where I am doing
wrong? I have used the following pull code:
Actual numbers would help. Is your initial configuration simply split across
periodic boundaries? If the initial distance is roughly equivalent to one of
the box vectors, then that's the case. Otherwise, please provide real data and
check to make sure your pull groups are what you think they are.
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
Note that you're not actually pulling along Y as you state above. Here, you're
pulling along Z. Perhaps that's one issue.
-Justin
pull_start = yes
pull_init1 = 0.0
pull_ngroups = 1
pull_group0 = dimer_ref ; reference group (based on
index file)
pull_group1 = dimer_pull ; pull group
pull_rate1 = 0.1
pull_k1 = 1000
pull_nstfout = 10
pull_nstxout = 10
best regards,
Shilpi Chaurasia
--
========================================
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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