[gmx-users] Pull code

[Gavin Melaugh]

Hi Justin

Thanks for your help. The two molecules are now moving together. I am
however slightly confused about the parameters pull_rate1 and pull_k1. I
want the molecules to come together very slowly therefore
I would set the rate to be a very small value. How the does the force
come into play and how should you decide on the best value?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Thanks. If I use the pull_geometry = direction I would go for the
>> following jus t to pull the molecules together in the z direction.
>>
>> pull        = umbrella
>> pull_geometry = direction
>> pull_start = yes
>> pull_ngroups = 1
>> pull_group0 = cage_1
>> pull_group1 = cage_2
>> pull_vec1 = 0.0 0.0 -1.0
>> pull_rate1 = 0.01
>> pull_k1 = 1000
>>
>>
>> Does this seem reasonable? Also in the pull_rate what is meant by the
>
> Probably.  Try it.
>
>> 'rate of change of the reference position'? (Is it the position of the
>> reference group, if so what if I don't want it to change?)
>>
>
> It is the rate of change of the reference position, which is the
> position at the outset of the simulation.  Your objective is to pull
> your two species together, right?  I don't see why you wouldn't want
> it to change.  You're not changing anything about pull_group0 (your
> reference group), since you aren't setting pull_rate0.  Everything is
> applied to pull_group1 (hence _rate1, _k1, etc).
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>