Hi Marcos,
I tried as you said, unfortunately it doesn't work. I got these two error
messages when submitting the script:
"
Name "main::wd" used only once: possible typo at
./prepare_runs_0-90-modified.perl line 3.
Preparing input files
Processing dihedral: 0
Can't exec "qsub": No such file or directory at
./prepare_runs_0-90-modified.perl line 27.
Processing dihedral: 3
"
The "Can't exec .." is repeated for all runs till dihe=90. ( here is the
files modified)
Do you think I should change the qsub command when preparing the input
files, if so how ?
Note I simply renamed ala_tri.rst file with 03_prod_60. Your help is
really appreacited.
Emanuele
Il giorno gio 27 set 2018 alle ore 14:56 emanuele falbo <
falbo.emanuele.gmail.com> ha scritto:
> 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/
>
>
--
*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 - 07:30:04 PDT
