[gmx-users] gromacs pullcode

[Justin Lemkul]

On 7/31/19 4:20 AM, zhaox wrote:
> Hi,
> There are two  groups in my system.When I use the pull code to pull 
> one group along the axis X, setting pull_coord1_geometry 
> =direction-periodic,I am confused with the "distance at start" and the 
> "reference at t=0".Could anyone can tell me how to understand 
> these?And if I use the absolute reference,how to understand these? For 
> example,when I set the pull_coord1_origin=0 0 0，how to calculate 
> “distance at start”？
> Thank you in advance.

I answered this exact question some time ago:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-July/125833.html

-Justin

> My pull code is followed:
> ; Pull code
> freezegrps          = bot    top
> freezedim           = Y Y Y  n y n
> pull                = yes
> pull_ncoords        = 2         ; two reaction coordinates x and z
> pull_ngroups        = 2         ; one group defining one reaction 
> coordinate
> pull_group1_name    = top
> pull_group2_name    = bot
> pull_coord1_type    = umbrella    ;harmonic potential
> pull_coord1_geometry= direction-periodic
> pull_coord1_vec     = 1 0 0
> pull_coord1_origin  = 0 0 0
> pull_coord1_groups  = 0 1
> pull_coord1_start   = yes
> pull_coord1_k       = 4000
> pull_coord1_rate    = 0.005
>
> pull_coord2_type    = constant-force
> pull_coord2_geometry= distance
> pull_coord2_dim     = n n y
> pull_coord2_groups  = 1 2
> pull_coord2_start   = yes
> pull_coord2_k       = 3838550        ;KJ mol^-1 nm^-1
>
> pull_group1_pbcatom  = 5806
> ;pull_group2_pbcatom  = 1887
> pull-pbc-ref-prev-step-com = yes
>
>
>
> cos-acceleration    = 0.05
> comm-mode            = linear
> nstcomm              = 10
> comm-grps            =
>
> 	
> zhaox
> zhaox at nuaa.edu.cn
>
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>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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