[gmx-users] Fwd: Questions for the forum

Matilde Viegas matildefrviegas at gmail.com
Thu Oct 13 16:51:39 CEST 2016 

Thank you Mark, will look into that!

2016-10-13 15:45 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Do check out gmx editconf -h for what it says about -d. Hint, that isn't
> setting the box dimensions directly, which is why you're getting a much
> bigger box.  Look also at the output of editconf, which will tel lyou that
> it's too big.
>
> Mark
>
> On Thu, Oct 13, 2016 at 4:39 PM Matilde Viegas <matildefrviegas at gmail.com>
> wrote:
>
> > I started with a pdb file of the protein, 5000 residues, no solvent,
> > crystallographic structure.
> >
> > Generated the .gro file, opting for the AMBER99SB force field (option 5):
> >
> > gmx pdb2gmx -f YYY.pdb -o YYY_GROMACS.gro -water tip3p -ignh (opted
> > for ignh as I was having trouble with differences in nomemclature)
> >
> > defined box:
> >
> > gmx editconf -f YYY_GROMACS.gro -o YYY_newbox.gro -c -d 1.2 -bt
> > dodechaedron
> >
> > solvation:
> >
> > gmx solvate -cp YYY_GROMACS_newbox.gro -cs spc216.gro -o
> > YYY_GROMACS_newboxsolv.gro -p topol.top
> >
> > add ions:
> >
> > gmx grompp -f ions.mdp -c YYY_newboxsolv.gro -p topol.top -o ions.tpr
> >
> > gmx genion -s ions.tpr -o YYY_newboxsolv_ions.gro -p topol.top -pname
> > NA -np 76 (the charge was -76)  (chose group 13 like the tutorial,
> > SOL)
> >
> >
> > at this point, my topol is:
> > [ molecules ]
> > ; Compound        #mols
> > Protein_chain_X     1
> > SOL         766582
> > NA               76
> >
> > and from this point i went on with minimization and so on.
> >
> >
> >
> > 2016-10-13 14:49 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 10/13/16 9:45 AM, Matilde Viegas wrote:
> > >
> > >> Of course, sorry!
> > >> I followed your lyzosyme tutorial, the exact same commands, only
> > addapting
> > >> it to my system (force field, tip3p water, just like I did on AMBER),
> > box
> > >> was dodechaedron, 1.2nm. I didn't alter anything beside that... My
> > enzyme
> > >> is around 72 thousand atoms, after adding the solvation box, it goes
> up
> > to
> > >> 2.5 million atoms.
> > >>
> > >>
> > > You need to provide your exact commands, copied and pasted from the
> > > terminal. You can't just say you did my tutorial, because there's a lot
> > of
> > > differences in what you actually did and what's in that example.
> > >
> > > One thing that is unclear is if you're trying to import an
> > > already-solvated system from AMBER into GROMACS.  If you are, then you
> > > shouldn't be re-sizing the box or adding any more water.  But again,
> only
> > > your exact commands and descriptions of file contents will tell us
> > anything
> > > productive.
> > >
> > > -Justin
> > >
> > >
> > > 2016-10-13 14:40 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> > >>
> > >>
> > >>>
> > >>> On 10/13/16 9:38 AM, Matilde Viegas wrote:
> > >>>
> > >>> Yes, I noticed that! I said 10, referring to angstrom, in the input I
> > had
> > >>>> 1.0nm.
> > >>>>
> > >>>> So you probably think it is only some error in the input, not really
> > >>>> something I can tackle, right? I really can't figure it out...
> > >>>>
> > >>>>
> > >>>> Without seeing your exact sequence of commands, there's nothing we
> can
> > >>> do
> > >>> to help.  The only thing consistent with having an unexpected
> > >>> million-atom
> > >>> system is that you set up the box incorrectly with editconf.  But you
> > >>> haven't told us exactly what you've done...
> > >>>
> > >>> -Justin
> > >>>
> > >>>
> > >>> Thank you for your time, Justin
> > >>>
> > >>>>
> > >>>> 2016-10-13 13:04 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> > >>>>
> > >>>>
> > >>>>
> > >>>>> On 10/13/16 7:34 AM, Matilde Viegas wrote:
> > >>>>>
> > >>>>> I tried to downzise to 10 and yet the reduction was very little. I
> > was
> > >>>>>
> > >>>>>> just
> > >>>>>> trying t understand how can the difference between the same
> systems,
> > >>>>>> using
> > >>>>>> either AMBER or GROMACS, can be of 1 million atoms...
> > >>>>>>
> > >>>>>>
> > >>>>>> GROMACS uses SI units, so distances/box vectors are specified in
> nm,
> > >>>>>> not
> > >>>>>>
> > >>>>> Angstrom.  See Chapter 2 of the manual for unit conventions.
> > >>>>>
> > >>>>> -Justin
> > >>>>>
> > >>>>>
> > >>>>> 2016-10-13 12:27 GMT+01:00 Dd H <ddhecnu at gmail.com>:
> > >>>>>
> > >>>>>
> > >>>>>> You can reduce your box size to get a smaller system.
> > >>>>>>
> > >>>>>>
> > >>>>>>> On 13 October 2016 at 17:41, Matilde Viegas <
> > >>>>>>> matildefrviegas at gmail.com
> > >>>>>>>
> > >>>>>>>>
> > >>>>>>>> wrote:
> > >>>>>>>
> > >>>>>>> Hi,
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>> my name is Matilde. This is my first time using GROMACS. I'm
> > >>>>>>>> switching
> > >>>>>>>>
> > >>>>>>>> from
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>> AMBER to GROMACS however I'm having some trouble reproducing my
> > >>>>>>> system:
> > >>>>>>>
> > >>>>>>>>
> > >>>>>>>> In AMBER, I'm working with a 5000 residues protein, a water box
> > >>>>>>>> (TIP3)
> > >>>>>>>> of
> > >>>>>>>> 12A, roughly 1.5 million atoms total. I tried building the same
> > >>>>>>>> system
> > >>>>>>>> in
> > >>>>>>>> GROMACS, cubic box, 12A, same protein, however I obtain a 2.5
> > >>>>>>>> million
> > >>>>>>>>
> > >>>>>>>> atoms
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>> system. Is there a way I can reduce the number of atoms?
> > >>>>>>>
> > >>>>>>>>
> > >>>>>>>> Thank you in advance,
> > >>>>>>>> Matilde
> > >>>>>>>> --
> > >>>>>>>> Gromacs Users mailing list
> > >>>>>>>>
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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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> > >>>>>
> > >>>>>
> > >>>>> --
> > >>> ==================================================
> > >>>
> > >>> 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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> > >>>
> > >>>
> > > --
> > > ==================================================
> > >
> > > 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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