Re: help regarding NAMD equilibration

From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Tue Apr 15 2008 - 01:05:25 CDT

Hi Snoze,

I can only answer the 2nd question because I don't have enough
experience with simulations to speak about the need for /importance of
constraints. If I read the gramicidin A tutorial correctly, the
Langevin temperature control is already on, that's why there's no need
to set langevin on again in your pasted code. LangevinPiston, on the
other hand, is the pressure control. It was turned off one line before
the code you pasted. In other words, it's minimize for 1000 steps, then
don't fix atoms and minimize another 1000 steps, as you say.
Minimization is a temperature-independent pressure-independent process.
And then heat up to your desired temperature for 3000 steps (remember
that langevin is already on but langevinPiston is still off - this means
that your system is under NVT i think). Then langevinPiston is turned
on to apply your pressure control so that it is now an NPT simulation -
the volume can change to suit the pressure control being applied now. I
think constraintScaling 0 is the _immediate_ removal of all constraints
that were applied earlier.

Cheers,
Soo Mei

snoze pa wrote:
> Deat NAMD users,
>
> I was going through the script in NAMD website to build Gramicidin A.
> I have a question related to equilibration part.
>
> 1. For every protein do I have to calculate "Fix Backbone Atoms" and
> "Restrain CA Atoms"
> 2. Anybody can explain me the meaning of following code. I am reading it as:
>
> mininize for 1000 step, then don't fix atom and minimize another 1000
> step, Lengevin off and run another 3000 step,
> Lengevin on and run another 5000 steps, and finally constraint
> scaling for 10000 runs.
>
> Thanks you
>
>
> # minimize nonbackbone atoms
> minimize 1000
> output min_fix
>
> # min all atoms
> fixedAtoms off
> minimize 1000
> output min_all
>
> # heat with CAs restrained
> # langevin on
> run 3000
> output heat
>
> # equilibrate volume with CAs restrained
> langevinPiston on
> run 5000
> output equil_ca
>
> # equilibrate volume without restraints
> constraintScaling 0
> run 10000
>
>

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