[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations
jalemkul at vt.edu
Sat Dec 15 19:44:29 CET 2012
On 12/15/12 4:03 AM, mircial at 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.
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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