[gmx-users] Re: Umbrella Sampling - Justin tutorial

[Steven Neumann]

Hi Justin,

I am sorry for so many questions but I do not understand something.
First we run the simulation of pulling Chain A from ChainB with constant
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
extract windows as we discussed and then run simulations with those
configurations as a starting point. I saw the trajectory of one of these
simulations and it looks like normal MD simulation. My question is: Why do
we have in mdp file still pull code as we do not pull protein chain any
more? Pull rate is set to zero but force is still applied... why? Is this
code just used to extract pullf.xvg and pullx.xvg which does not change too
much?
I would appreciate the explanation as without undesratnding the basics its
not good to do any simulation like this.

Thank you

Steven




Are my questions to trivial or noones knows? Please, help!

On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Hi GMX Users,
>
> I am doing Justin tutorial of Umbrella sampling. I have just finished
> continous pulling of chainA from the reference chainB. I have some
> questions. I looked at the trajectory of pulling and it has began with
> dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My
> question is why? As you apply pulling with the constant force to the COM of
> the whole chain why does it start with terminal residue following then one
> by one? Why not the middle one or any other?
>
> The second thing I would like to extract starting configurations from from
> my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
> as the ChainA is still within ChainB. I would like to use configurations:
>
> 0 - 0.50
> 50 - 0.52
> 100 - 0.51
> 150 - 0.51
> 200 - 0.62
> 250 - 2.21
> ....
> 500 - 5.48
>
> My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
> this configuration above is ok? Can the spacing in nm vary?
> And the last thing - is it required to use frames till 189 as the COM
> varies in this area?
>
> Thank you!
>
> Steven
>
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