[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Sat Dec 15 10:03:55 CET 2012

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? 
(2)Also, does anyone know which value is used in the umbrella sampling simulations, the grompp result or the g_dist result?
(3)how to choose the right starting conformations since there is such a difference? 

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

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