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

[Justin Lemkul]

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.

-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

========================================