Hi, The -neutral option of genion should do the trick
Cheers Tom ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of João Henriques [joao.henriques.32...@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 <samuelflor...@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 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.