[gmx-users] auto-neutralize system

[Justin Lemkul]

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

==================================================