[gmx-users] auto-neutralize system
Mark Abraham
mark.j.abraham at gmail.com
Fri Feb 19 22:50:16 CET 2016
Hi,
On Fri, Feb 19, 2016 at 10:38 PM Samuel Flores <samuelfloresc at gmail.com>
wrote:
> I’m using 5.1.1 , so I guess -neutral alone should work for me.
>
> Does this just add the minimum number of ions needed to neutralize the
> system? So for a net-neutral protein (even with several charged residues)
> no ions would be added?
>
Trying it, or gmx genion -h or
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-genion.html is
faster than email :-)
Mark
thanks
>
> Sam
>
> > On Feb 19, 2016, at 12:33, Piggot T. <T.Piggot at soton.ac.uk> wrote:
> >
> > 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-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin
> Lemkul [jalemkul at vt.edu]
> > Sent: 19 February 2016 11:24
> > To: gmx-users at 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.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
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> posting!
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> >>>>
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> >>>>
> >>> --
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> >
> > --
> > ==================================================
> >
> > 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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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>
> Samuel Coulbourn Flores
> Associate Professor
> Computational and Systems Biology Program
> Department of Cell and Molecular Biology
> Uppsala University
>
> --
> Gromacs Users mailing list
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