On Mon, Dec 21, 2015 at 8:36 AM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> Thank you,
>
> I understand that includes equilibration, heating everything which has
> ntt=3 ?
>
> So why for example in tutorial 3 section two there is this example:
>
> ~prod ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=250000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
> Which obviously does not use ig at all?
>
It's an oversight. This tutorial is rather old and the focus of the
tutorial is on running MM/PBSA analyses moreso than the dynamics. It
should still be improved, so I've added this variable to the input files
and it should be reflected next time the website is updated.
Thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 21 2015 - 07:00:04 PST
