Re: help regarding NAMD equilibration

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Apr 15 2008 - 10:39:54 CDT

Thanks a lot Low and Jacob. I highly appreciate your help.

On Tue, Apr 15, 2008 at 2:05 AM, Low Soo Mei <lowsm_at_bii.a-star.edu.sg> wrote:
>
> 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
>
>
>

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