[gmx-users] Fwd: Questions for the forum

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Thu Oct 13 17:23:12 CEST 2016 

You probably want to use -box 1.2 1.2 1.2 rather than -d 1.2.

Best wishes
James

> 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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>> > >>>>>>>> --
>> > >>>>>>>>
>> > >>>>>>>> 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
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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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>> > >>>
>> > >>>
>> > > --
>> > > ==================================================
>> > >
>> > > 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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