[gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:

> I will ty Justin's suggestion. I should have the answer by tomorrow.
> As for Thomas' suggestion, well, my mdp file didn't even have the 
> "pull_start" flag. So I assume gromacs though I had set it to "no". But 
> anyway, I checked the force in each window as you mentioned andfound 
> something quite strange. The original pull_pf.xvg file, is an eve 
> increasing line starting at -43 kj/mol/nm. So when I check a specific 
> time frame, the pull force is, for example 93 kj/mol/nm at time frame 
> 4000. But when I checked the pull force on the pull_pf.xvg file at that 
> specific window, well, the pull force was something around -42 
> kj/mol/nm. Now I am really confused. It seems I am doing something 
> really wrong, but actually quite simple to solve. I will try setting 
> "pull_start = yes" and see what happens.

Because you're looking at two entirely different things.  In your initial 
pulling simulation to separate your species, the force will continually change, 
building up until the two dissociate, then probably level off to some roughly 
constant value until the simulation stops (when the species are no longer 
interacting).

In umbrella sampling, the force imposed on the pull group is used to restrain it 
within a window, and will not necessarily have anything to do with the values 
obtained in the original separation simulation.  Apples to oranges, if you will.

Setting "pull_start = yes" is appropriate for the umbrella sampling.  In 
conjunction with "pull_init1 = 0" the original distance between the two species 
should be taken as the distance to be restrained during umbrella sampling 
simulations.

> One other thing. I checked my pull_px.xvg file for the initial 
> separation trajectory. It looks like a a rollercoaster with a tendency 
> to going down. So the final value of distance PULL_COM is 1.5nm lower 
> than the initial value. The values on each of my windows are the same 
> for the individual values pf the separation trajectory from which they 
> were taken. And again, the values on the pull_px,xvg files all decrease.
> 

Not a steady increase as the two species separate?  Is your box size sufficient 
to accommodate the distance you are pulling, or are you experiencing periodicity 
artefacts?

> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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