[gmx-users] auto-neutralize system

Samuel Flores samuelfloresc at gmail.com
Fri Feb 19 22:38:19 CET 2016 

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?

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
>>>> 
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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

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