Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Dec 15 2010 - 11:07:20 CST

On 15 December 2010 17:34, Ajasja Ljubetińć <ajasja.ljubetic_at_gmail.com> wrote:
>
> Dear J√©r√īme,
> >Interesting that you should ask now.
> This is great :)
> I have just a few questions about the input script.
> harmonic {
>  colvars chi
>  centers -70
>  targetCenters 290
>  targetNumSteps  10000
>  targetNumStages 36
>  forceConstant 0.5
> }
> In the NAMD input, do I have to specify  "minimize 3600000"? And for normal SMD "run 3600000"?

Actually 3700000, including the last stage, which repeats the first
one (useful to check for hysteresis). 10000 steps might not be needed
for convergence, but the restraints seem to make it slower than a
standard minimization.

> Will this really preform a full turn or just from -70 to 290 degree?

That *is* a full turn :-)

> It currently says in the manual:
> "if a complete 360 turn of a dihedral is desired, multiple runs (at least two) with different targets should be used."

This has changed in CVS. The starting and target values are not
wrapped automatically anymore.

> >You are also assuming that the change in average energy is mirrored by
> >the change in minimum energy.
> Yes, I forgot about that. So in theory running the ABF scan at different temperatures could be used to get the entropic contribution?

Or you can run restrained, standard MD and measure average energies,
but this is going to be noisy. In my opinion, the approximation of
using the PES is not too bad.

> I have another (unrelated) question that has been bugging me.
> Do you (or anybody reading this) happen to know  which compiler is used for the official (windows) NAMD binaries?

No idea. You should post this as a separate message, because no one is
going to notice it in here.

Cheers,
Jerome

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