[gmx-users] auto-neutralize system

[João Henriques]

Does it work without specifying -nn and -np? I thought it added on top of
the ions specified with -np/-nn or -conc, but I am likely to be wrong.

/J

On Fri, Feb 19, 2016 at 12:18 PM, Piggot T. <T.Piggot at soton.ac.uk> wrote:

> Hi,
>
> The -neutral option of genion should do the trick
>
> Cheers
>
> Tom
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of João
> Henriques [joao.henriques.32353 at gmail.com]
> Sent: 19 February 2016 11:07
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] auto-neutralize system
>
> Not that I know of. Anyway, that's like a couple of extra line of code...
> Just read the topology and parse the total charge (that's a one-liner in
> awk, for example). Then, depending on whether it's positive, negative or
> zero, you just set two variables with the correct integer(s) and feed it to
> genion like so:
>
> genion ... -np $var1 -nn $var2
>
> Imagine the net charge is +5, then var1=0 and var2=5.
>
> Put this inside a function and you use it over and over without having to
> write more code.
>
> /J
>
> On Fri, Feb 19, 2016 at 11:37 AM, Samuel Flores <samuelfloresc at gmail.com>
> wrote:
>
> > Guys,
> >
> > Is there a way  you know a way to avoid using e.g. -np to explicitly
> > specify number of ions? I would prefer to let GROMACS figure out how many
> > ions it needs to neutralize the system. Mostly this is because I am
> writing
> > a script to generate SLURM job files for a bunch of variants, and adding
> up
> > the charges means more coding for me. My system is Staphylococcal
> Protein A
> > , domain B, in solvent.
> >
> > I append below the sort of job file I would be having my script generate.
> >
> > Many thanks
> >
> > Sam
> >
> >
> >
> > #!/bin/bash -l
> > #SBATCH -J BF18
> > #SBATCH -p node
> > #SBATCH -n 16
> > #SBATCH -N 1
> > #SBATCH --exclusive
> > #SBATCH -A snic2015-1-443
> > #SBATCH -t 72:00:00
> >
> >
> > module add gromacs/5.1.1
> > cd /home/samuelf/projects/SpA-ZEMu-method-upgrade/C-130-F
> > # was /proj/snic2015-1-317/GROMACS/GROMACS/BF-SPA/C-130-F/
> > echo 6 > temp.txt
> > echo 1 >> temp.txt
> >
> > cat temp.txt | gmx_mpi pdb2gmx -f last.2.pdb -o last.2_processed.gro
> -ignh
> > #6: Amber sb99 , 3 point TIP3P water model: force field was selected
> based
> > on this benchmark article:
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/ <
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/>
> > gmx_mpi editconf -f last.2_processed.gro -o last.2_newbox.gro -c -d 1.0
> > -bt cubic
> > gmx_mpi solvate -cp last.2_newbox.gro -cs spc216.gro -o last.2_solv.gro
> -p
> > topol.top
> >
> > gmx_mpi grompp -f ions.mdp -c last.2_solv.gro -p topol.top -o ions.tpr
> > echo 13 | gmx_mpi genion -s ions.tpr -o last.2_solv_ions.gro -p topol.top
> > -pname NA -np 5
> > mpirun -np 16 gmx_mpi grompp -f minim.mdp -c last.2_solv_ions.gro -p
> > topol.top -o em.tpr
> > mpirun -np 16 gmx_mpi mdrun -v -deffnm em
> >
> > gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
> > mpirun -np 16 gmx_mpi mdrun -deffnm nvt
> > gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
> > mpirun -np 16 gmx_mpi mdrun -deffnm npt
> > gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
> > mpirun -np 16 gmx_mpi mdrun -deffnm md_0_1
> >
> >
> > Samuel Coulbourn Flores
> > Associate Professor
> > Computational and Systems Biology Program
> > Department of Cell and Molecular Biology
> > Uppsala University
> >
> > --
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