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.abra...@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 >> <matildefrvie...@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 <jalem...@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 <jalem...@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 <jalem...@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 <ddhe...@gmail.com>: >> > >>>>> >> > >>>>> >> > >>>>>> You can reduce your box size to get a smaller system. >> > >>>>>> >> > >>>>>> >> > >>>>>>> On 13 October 2016 at 17:41, Matilde Viegas < >> > >>>>>>> matildefrvie...@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 >> > >>>>>>>> >> > >>>>>>>> * 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 >> > >>>>>>>> >> > >>>>>>>> * For (un)subscribe requests visit >> > >>>>>>>> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> > >>>>>>>> or >> > >>>>>>>> send a mail to gmx-users-requ...@gromacs.org. >> > >>>>>>>> >> > >>>>>>>> -- >> > >>>>>>>> >> > >>>>>>>> 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 >> > >>>>>>> >> > >>>>>>> * For (un)subscribe requests visit >> > >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_ >> gmx-users >> > >>>>>>> or >> > >>>>>>> send a mail to gmx-users-requ...@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 >> > >>>>> >> > >>>>> jalem...@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 >> > >>>>> >> > >>>>> * For (un)subscribe requests visit >> > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> > or >> > >>>>> send a mail to gmx-users-requ...@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 >> > >>> >> > >>> jalem...@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 >> > >>> >> > >>> * For (un)subscribe requests visit >> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> > >>> send a mail to gmx-users-requ...@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 >> > > >> > > jalem...@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 >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> > > send a mail to gmx-users-requ...@gromacs.org. >> > > >> > -- >> > 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 >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> 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 >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.