In fact, from a very quick test in 4.5.7 -neutral has to be provided with -conc (or -np -nn) but in 5.0.6 -neutral seems to work on its own.
Cheers Tom ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 19 February 2016 11:24 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] auto-neutralize system On 2/19/16 6:23 AM, João Henriques wrote: > 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. > This is what the documentation says, and unless the code has been changed, I recall finding that using -neutral on its own has no effect (would be a lovely feature to have, though). -Justin > /J > > On Fri, Feb 19, 2016 at 12:18 PM, Piggot T. <t.pig...@soton.ac.uk> wrote: > >> 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. >> -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.