thanks for promptly replying Marcos.
I will give it a try and then let you know. Thanks again.
Cheers,
Emanuele
Il giorno gio 27 set 2018 alle ore 14:52 Marcos Serrou do Amaral <
marcossamaral.gmail.com> ha scritto:
> Dear Emanuele,
>
> You could try to change the write_batchfile function and try something like
> this:
>
> sub write_batchfile {
> open BATCHFILE, '>', "run.$dihed.sh";
> print BATCHFILE <<EOF;
>
> #!/bin/bash
>
> mpirun -np 2 pmemd.MPI -O \\
> -i mdin_min.$dihed -p ${name}.prmtop -c ala_tri_prod_60.rst -r
> ${name}_min_${dihed}.rst -o ${name}_min_${dihed}.out
> mpirun -np 2 pmemd.MPI -O \\
> -i mdin_equi.$dihed -p ${name}.prmtop -c ${name}_min_${dihed}.rst -r
> ${name}_equil_${dihed}.rst -o ${name}_equil_${dihed}.out
> mpirun -np 2 pmemd.MPI -O \\
> -i mdin_prod.$dihed -p ${name}.prmtop -c ${name}_equil_${dihed}.rst -r
> ${name}_prod_${dihed}.rst -o ${name}_prod_${dihed}.out -x
> ${name}_prod_${dihed}.mdcrd
> EOF
>
> print BATCHFILE "\necho \"Execution finished\"\n";
> close BATCHFILE;
> }
>
> Good luck!
> ---
> Marcos S.A.
>
>
>
> On Thu, Sep 27, 2018 at 9:34 AM emanuele falbo <falbo.emanuele.gmail.com>
> wrote:
>
> > Dear users,
> >
> > I am following the umbrella sampling tutorial on the web site
> > http://ambermd.org/tutorials/advanced/tutorial17/section2.htm .
> > I got a bit stuck when using the perl scripts for running all the
> > calculations., because I would like to use these scripts (here is
> attached
> > one type.) for running the calculations in parallel on my workstation (
> it
> > is not a cluster).
> >
> > So , I am wondering if anybody knows the way to modify them and get the
> > calculations done successfully.
> >
> > Best Regards
> >
> >
> >
> > --
> >
> > *Emanuele Falbo*
> > PhD student
> > Penfold group
> > School of Natural and Environmental Sciences
> > Bedson Building, Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> > w: http://tompenfoldresearch.weebly.com/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Thu Sep 27 2018 - 07:00:02 PDT
