ok I figured it out
The same equilibration starting structure is used for all of the
simulations (the one generated in the previous section).
On Mon, Oct 26, 2015 at 10:07 AM, Hadeer ELHabashy <
hadeer.elhabashi.gmail.com> wrote:
>
> Dear Sir
>
> wish you are fine !
> when I was try to reproduce tutorial 18 of the constant ph md
> I found the following command of the production run
>
> $AMBERHOME/bin/mpiexec -f $PBS_NODEFILE sander.MPI -O -i pH_<*pH*>.mdin
> -p 4LYT.parm7 -c 4LYT.equil.rst7 -cpin 4LYT.equil.cpin -o <*pH*>/4LYT.md1.mdout
> -cpout <*pH*>/4LYT.md1.cpout -r <*pH*>/4LYT.md1.rst7 -x <*pH*>/4LYT.md1.nc
> -cprestrt <*pH*>/4LYT.md1.cpin
>
> This command does not change the restart file at the beginning of each new
> run with different constant ph "-c 4LYT.equil.rst7 "
> Is that correct or I should change it to -c <ph>/4LYT.rst7
>
> Regards
>
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Received on Mon Oct 26 2015 - 01:30:04 PDT
