[gmx-users] gromacs pullcode

[Justin Lemkul]

On 7/6/19 9:17 PM, 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,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

Reference at t0 refers to the COM position of group1. Distance at start 
is the COM distance between the two groups.

> example,when I set the pull_coord1_origin=0 0 0,what means the 
> "distance at start"?

This should be the same concept, except that rather than having a 
reference that is the COM of a specified group, it is the coordinate origin.

> Thank you in advance.
> My pull code is followed:
> ; Pull code
> freezegrps          = bot    top
> freezedim           = Y Y Y  N N  N
> pull                = yes
> pull_ncoords        = 1           ; only one reaction coordinate
> pull_ngroups        = 2           ; one group defining one reaction 
> coordinate
> pull_group1_name    = top
> pull_group2_name    = bot
> pull_coord1_type    = constant-force
> pull_coord1_geometry= direction
> ;pull_coord1_origin  =
> pull_coord1_vec     = 1 0 0
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes
> ;pull_coord1_rate    = -0.0001
> pull_coord1_dim     = y n n

Note that pull_coord1_dim is not used with "direction" geometry.

-Justin

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Justin A. Lemkul, Ph.D.
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