[gmx-users] Fwd: Questions for the forum

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 13 16:45:35 CEST 2016 

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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> >>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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> >>>>>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >>>>>>>> or
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> >>>>>>>>
> >>>>>>>> --
> >>>>>>>>
> >>>>>>>> Gromacs Users mailing list
> >>>>>>>
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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
> >>>>>
> >>>>> ==================================================
> >>>>>
> >>>>> --
> >>>>> 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
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> or
> >>>>> send a mail to gmx-users-request at 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
> >>>
> >>> jalemkul at 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
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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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
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