On 12/15/12 4:03 AM, mirc...@sjtu.edu.cn wrote:
Dear All:
I encountered a problem when doing umbrella sampling. The distance calculated
by grompp and g_dist is different, as shown by the following:
grompp z component of g_dist(since I am constraining the distance between two
groups along the z direction, I should calculate the z component of the
distance, right?)
2.986 2.96
2.953 2.95
2.931 2.92
2.936 2.9355
2.844 2.83
There is an obvious difference between the distance calculated by the grompp
and the g_dist, I also found that some post similar problems in the maillist,
but I didn't found answers for the following questions.
(1)Why there is a such difference?
Probably because the default pull_pbcatom1 doesn't represent your pulled group
very well. By default, the atom is chosen as the numerical middle, which may
not correspond to the geometric middle in a complex molecule.
(2)Also, does anyone know which value is used in the umbrella sampling
simulations, the grompp result or the g_dist result?
Whatever grompp tells you is what is used.
(3)how to choose the right starting conformations since there is such a
difference?
More likely, you should start by defining pull_pbcatom1 more appropriately.
-Justin
I also pasted the pull code I used as follows:
pull = umbrella
pull_geometry = direction
pull_dim = N N Y
pull_start = yes
pull_nstxout = 500
pull_nstfout = 500
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = AMA
pull_init1 = 0
pull_rate1 = 0.000;nm/ps
pull_k1 = 4500 ;kJ/mol/nm^2
Thanks in advance!!
Best regards,
Ruo-Xu Gu
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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