Re: [AMBER] cpptraj.MPI query

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Mon, 4 Nov 2019 15:34:59 +0000

Okay,this is the content of my distance_299.in file


parm ~/setup_solvbox/pdb_layer_IPA_H2O_5-95vv.prmtop
trajin New4A_production.1.crd 1 1250 1
trajin New4B_production.1.crd 1 1250 1
trajin New4C_production.1.crd 1 1250 1
trajin New4D_production.1.crd 1 1250 1
trajin New4E_production.1.crd 1 1250 1
trajin New4F_production.1.crd 1 1250 1
trajin New4G_production.1.crd 1 1250 1
trajin New4H_production.1.crd 1 1250 1
trajin New4I_production.1.crd 1 5000 1
trajin New4J_production.1.crd 1 5000 1
strip :WAT
strip :Na+

solvent pdb_layer_IPA_H2O_5-95vv.prmtop none

reference PDB_layer_IPA_H2O.pdb

rms reference mass out IPA_299_RMSD.txt :1-274.CA

distance IPA_site1_RUN1 :299.C2 point -3 -0.875 7.25 noimage out distance_299_site1_RUN1.out
distance IPA_site2_RUN1 :299.C2 point -15.25 -4.75 -24.375 noimage out distance_299_site2_RUN1.out
go























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________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Monday, November 4, 2019 10:20:00 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj.MPI query

Sorry, I mean what is in e.g. 'distance_1.in'?

-Dan

On Mon, Nov 4, 2019 at 9:02 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi.
>
> These are the contents of the script:
> #! /bin/bash
> #SBATCH -J distance_on-off_IPA_xac
> #SBATCH --partition=cluster1
> #SBATCH --array=1-29%2
> #SBATCH -n 8 # This means 8 core jobs will be running..
>
> ###############################################################
> export submit_dir=/users/debarati/CHK_Kinase/ON_OFF/IPA/$1
> cd $submit_dir
> echo Working Directory = $submit_dir
>
> echo Hostname = `hostname -s`
>
> echo Date = `date`
>
> export AMBERHOME=/usr/local/amber18
> export MPI_HOME=/usr/local/mpich-3.2.1
> export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH
>
> name=$(awk -F "_" '{print $2}' "$2"| sed 's:.in::g')
>
>
> for x in `cat xac`;
> do $MPI_HOME/bin/mpiexec -n 8 cpptraj.MPI -i "$x"
> done
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> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Sunday, November 3, 2019 8:00:50 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] cpptraj.MPI query
>
> If you just run cpptraj.MPI with distance_1.in, does it complete normally?
> What commands are in that script?
>
> -Dan
>
> On Sun, Nov 3, 2019 at 12:39 PM Debarati DasGupta <
> debarati_dasgupta.hotmail.com> wrote:
>
> > Can we execute cpptra.MPI using a simple for loop in bash:
> >
> > Like, I have done this with cpptraj it works; but I cant get it to work
> > for cpptraj.MPI
> >
> > So when I type this:
> > For x in `cat list` ; do cpptraj<$x ; echo done for $x ; done
> >
> > I get my distances calculated.. list is actually 100 input files by the
> > name of distance_1.in distance_2.in distance_3.in .... so on till
> > distance_100.in
> >
> >
> > Now when I try doing the same thing for cpptraj.MPI
> >
> > While read x ;
> > do $MPI_HOME/bin/mpiexec -n 12 cpptraj.MPI -i $x ;
> > done<list
> >
> > It works for the first entry that is I get output for distance_1.in, but
> > not the other 99 input files..
> > Any reason what I am be doing wrong.
> > Just to let you all know, I have exported AMBERHOME, MPI HOME, and
> > LD_LIBRARY PATH properly in my slurm script...
> > Thanks
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 04 2019 - 08:00:02 PST
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