On Sat, Sep 2, 2017 at 1:07 PM, George Tzotzos <gtzotzos.me.com> wrote:
> It’s my first attempt at explicit solvent CpHMD. In summary, my objective
> is to predict whether structural changes of a protein-ligand complex
> brought about by changes in pH result in the release of the ligand. I
> intend to perform simulations at pHs 5, 6 and 7.
>
> As a starting point, I’m using the same md.in files described in
> http://jswails.wikidot.com/explicit-solvent-constant-ph-md <
> http://jswails.wikidot.com/explicit-solvent-constant-ph-md>
>
> I’ve successfully generated protein_solv.cpin which I then used in heating
> and equilibrating the system using the following input commands:
>
> (heat) $PMEMD -O -i heat.in -c subA.min.rst -p subA_solv.modO.prmtop -ref
> subA.min.rst -cpin subA_solv.cpin -o subA.heat.out -r subA.heat.rst -x
> subA.heat.nc
>
> (equilibration) $PMEMD -O -i equil.in -p subA_solv.modO.prmtop -c
> subA.heat.rst -cpin subA_solv.cpin -o subA.equil.out -cpout
> subA.equil.cpout -r subA.equil.rst -x subA.equil.nc -cprestrt
> subA.equil.cpin
>
> In the equilibration step, I obtained the equil.out, equil.cpout,
> equil.rst, and equil.nc but NOT the expected equil.cpin
>
If you used the mdin file from my Wikidot page for equilibration, then you
never set icnstph=2. This means that the equilibration was *not* run at
constant pH, so no cprestart will be created (although no cpout should have
been created either).
HTH,
Jason
--
Jason M. Swails
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Received on Sun Sep 03 2017 - 05:00:02 PDT
