[gmx-users] AFM Pulling Rate

[kobi]

Hello Bob,

have you tried to define the initial position of the AFM-tip? It needs
to be set to the position of the COM of the group you want to pull. try
and add
    "afm_init1 = x y z"
(x y z = position where the afm should be) to your pull.ppa.
Otherwise your afmspring is extended from the beginning so much, that
this extension dominates the force on the pulling group and the
pullingrate is nearly irrelevant until the system relaxed.

ciao Jan
> Hello everyone,
> I am using AFM pulling to drag a dna base across the surface of a graphene. I'm
> doing this in vaccuum. It seems that the base is pulled at the same rate no
> matter what value I specify in afm_rate1. Here is my pull.ppa file:
>
> runtype = afm
> group_1 = ssdna-ions
> pulldim = N N Y
> afm_rate1 = 0.05
> afm_k1 = 100
> afm_dir1 = 0 0 1
>
> I'm using version 3.3. Does anyone know what's going on?
> Thanks,
> Bob Johnson
>
>