Re: [AMBER] Umbrella sampling scripts

From: Marcos Serrou do Amaral <marcossamaral.gmail.com>
Date: Thu, 27 Sep 2018 09:51:27 -0400

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
Received on Thu Sep 27 2018 - 07:00:02 PDT
Custom Search