Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

) > > Mark > > On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero <borregu...@gmail.com> > wrote: > > > Dear Gromacs users, > > > > I'm a relatively new user of Gromacs and recently realized there is a > > "2016" branch that is still being updated.

[gmx-users] what is the difference between the 2016.x and the 5.x series?

Dear Gromacs users, I'm a relatively new user of Gromacs and recently realized there is a "2016" branch that is still being updated. What is the difference with the 5.x branch? I ask because I could find RPM packages only for the 2016 version, much easier to install than building from source.

Re: [gmx-users] adding a custom residue with an itp file

Thanks, Justin. I suspected that was the case but I wanted to be 100% sure :D .Jose On Tue, Jun 27, 2017 at 9:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/27/17 12:32 PM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I have creat

[gmx-users] adding a custom residue with an itp file

Dear Gromacs users, I have created an include topology file (sil.itp) for a silica crystal, but the instructions in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field leave me with a couple of unclear points. Please help! 1. This "residue" is not of type 'Protein' or

Re: [gmx-users] adding new ion within the oplsaa force field

yes, the ions I have can be considered as bound. I found out I also had to declare the type of residue as "Ion" in file residues.dat :) On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/23/17 3:50 PM, Jose Borreguero wrote: > >

[gmx-users] adding new ion within the oplsaa force field

required? Best, Jose Borreguero -- 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

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

Victory! The -noparam did the trick :) Thanks a million. On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/21/17 11:39 AM, Jose Borreguero wrote: > >> Hi Justin, >> >> ​Thanks for your quick reply! ​ >> This m

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

lem...@vt.edu> wrote: > > > On 6/21/17 10:47 AM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I created the .top file for a small silica crystal that contains only two >> types of atoms, silicon (type SIO) and oxygen (type OSI). The bond >>

[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

Dear Gromacs users, I created the .top file for a small silica crystal that contains only two types of atoms, silicon (type SIO) and oxygen (type OSI). The bond potential is: [ bondtypes ] ; ij func b0 kb SIO OSI 1 ​ ​ 0.15783 ​ ​ 251040 After running gmx x2top,

Re: [gmx-users] How to parameterize the volume occupied by a protein?

olvating" with silica. You > may need to teach the tool about suitable atomic radii. See the the help > text. > > Mark > > On Sat, 17 Jun 2017 02:05 Jose Borreguero <borregu...@gmail.com> wrote: > > > Dear all, > > > > I have superimposed a protein o

[gmx-users] How to parameterize the volume occupied by a protein?

is inside the volume. Does anyone know how to parameterize the volume occupied by a protein? Best, Jose Borreguero. -- 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

[gmx-users] (Newbie) Residue SiO2 for solvation?

d then the steps to "merge" this residue with the rest of the OPLS force-field? Best. Jose Borreguero -- 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/Suppor

Re: [gmx-users] Remove all but N closest water molecules from protein

ach frame according to their > > distance to the protein. Then you either manually prune the gro file(s) > or > > use an index file to get rid of the extra stuff. I don't know of any > native > > tool that does all of this in one step but I may be outdated regarding > new > >

[gmx-users] Remove all but N closest water molecules from protein

Dear Gromacs users, I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow me to create a new *.gro file containing the protein and the N closest water molecules to the protein ​, starting from a system of a solvated protein​ ? Best, Jose Borreguero -- Gromacs Users mailing

Re: [gmx-users] Installation woe: fatal error: mpi.h: No such file or directory

ir -p $GROMACSDIR/install > mkdir -p $GROMACSDIR/build > cd $GROMACSDIR/build > cmake $GROMACSDIR -DGMX_MPI=ON -DGMX_BUILD_MDRUN_ONLY=ON > -DGMX_BUILD_OWN_FFTW=ON > -DCMAKE_INSTALL_PREFIX=/SNSlocal/sw/gromacs/gromacs-5.1.3/install > > If that works, then consider -DBUILD_SHARED_

[gmx-users] Installation woe: fatal error: mpi.h: No such file or directory

Dear GROMACS users, I don't know what's going on, installation "fails to find mpi.h" again and again. The error message: In file included from /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/legacyheaders/types/commrec.h:45:0, from