Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?
will do, thanks for the tip. On Wed, Jul 12, 2017 at 11:42 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > That kind of information is in the release notes, e.g. at > http://manual.gromacs.org/documentation/. Perhaps you want to start with > the 2016 ones :-) > > 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. 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. > > > > Best, > > .Jose > > -- > > 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.
[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. Best, .Jose -- 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.
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 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 'DNA', so can I just create >> a >> new type in file residuestypes.dat? Something like "SIL Silica"? Do I >> actually have to declare this molecule within residuestypes.dat? >> >> 2. All the bonding info is already in the sil.itp file I just created, but >> do I still have to include this residue in file aminoacids.rtp? >> >> > You only need aminoacids.rtp and residuetypes.dat if you're running > pdb2gmx. You already have a topology, so there is no purpose to running > pdb2gmx. > > -Justin > > -- > == > > 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.
[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 'DNA', so can I just create a new type in file residuestypes.dat? Something like "SIL Silica"? Do I actually have to declare this molecule within residuestypes.dat? 2. All the bonding info is already in the sil.itp file I just created, but do I still have to include this residue in file aminoacids.rtp? Best, Jose -- 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.
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: > >> Dear Gromacs users, >> >> I'm trying to add a new type of atom as an ion. Looking at already >> existing >> ions, such as sodium (NA), I see there's an entry both in files ions.itp >> and aminoacids.rtp. My question is, what is the rationale of declaring >> ions >> both as ions and as residues? Is this always required? >> >> > If you want to process it with pdb2gmx, you need an entry in an .rtp > file. If you just have an ion that you're going to add into a box, you can > rely on ions.itp. The current implementation covers both cases. Some > structures have bound ions and it makes life easier to be able to process > them with pdb2gmx. > > -Justin > > -- > == > > 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.
[gmx-users] adding new ion within the oplsaa force field
Dear Gromacs users, I'm trying to add a new type of atom as an ion. Looking at already existing ions, such as sodium (NA), I see there's an entry both in files ions.itp and aminoacids.rtp. My question is, what is the rationale of declaring ions both as ions and as residues? Is this always 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/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 means x2top is not finding >> >> or using >> the right force constant value, right? >> I >> >> >> did >> add the bond info into file ffbonded.itp >> of >> the oplsa.ff/ directory >> >> (https://goo.gl/z5UMot) >> . >> I also included the types in file >> atomtypes.atp >> >> and the non bonded info in >> ffnonbonded.itp file. Maybe related to this issue is this line also found >> in the output .top file: >> >> #include " >> >> ./oplsaa.ff/forcefield.itp" >> This line should not be necessary because the .top file contains all >> information. Does the line mean that the bond information in the output >> .top file is overridden with that gmx later finds under >> >> ./oplsaa.ff >> ? >> If so, then the particular value of the force constant in the .top file >> would be irrelevant and my problem would be solved! :) >> >> > Any value found in the .top overrides the force field. Any blank in the > topology is referenced from ffbonded.itp. Anything missing after that > generates a fatal error in grompp. Use -noparam when running x2top if > everything is accounted for in the force field parameter files. > > > -Justin > > -- > == > > 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.
Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top
Hi Justin, Thanks for your quick reply! This means x2top is not finding or using the right force constant value, right? I did add the bond info into file ffbonded.itp of the oplsa.ff/ directory (https://goo.gl/z5UMot) . I also included the types in file atomtypes.atp and the non bonded info in ffnonbonded.itp file. Maybe related to this issue is this line also found in the output .top file: #include " ./oplsaa.ff/forcefield.itp" This line should not be necessary because the .top file contains all information. Does the line mean that the bond information in the output .top file is overridden with that gmx later finds under ./oplsaa.ff ? If so, then the particular value of the force constant in the .top file would be irrelevant and my problem would be solved! :) .Jose .Jose On Wed, Jun 21, 2017 at 10:51 AM, Justin Lemkul <jalem...@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 >> potential is: >> [ bondtypes ] >> ; ij func b0 kb >>SIO OSI 1 >> >> 0.15783 >> >>251040 >> >> After running gmx x2top, the .top file contains >> [ bonds ] >> ; aiaj funct c0c1c2c3 >> 1 9 1 1.60e-01 4.00e+05 1.60e-01 4.00e+05 >> 135 1 1.60e-01 4.00e+05 1.60e-01 4.00e+05 >> >> I >> assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I >> was expecting number 251040 for c1 and c3, got >> >> 40 instead >> ! >> I don't know the meaning of coefficients c0, c1, c2, and c3 >> , >> I could not find some explanation for them >> . >> Can anyone point to a place where these coefficients are described in >> detail? The description may explain the >> >> 40 >> number. >> >> > > It's the default bonded force constant. > > gmx help x2top > " > ... > -kb (40) Bonded force constant (kJ/mol/nm^2) > ... > " > > The comment line means little, so there's no specific meaning to c0, c1, > etc. It generically refers to bonded parameter fields, which for bonds are > A- and B-state equilibrium lengths and force constants. For dihedrals > these mean something entirely different. > > -Justin > > -- > == > > 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.
[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, the .top file contains [ bonds ] ; aiaj funct c0c1c2c3 1 9 1 1.60e-01 4.00e+05 1.60e-01 4.00e+05 135 1 1.60e-01 4.00e+05 1.60e-01 4.00e+05 I assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I was expecting number 251040 for c1 and c3, got 40 instead ! I don't know the meaning of coefficients c0, c1, c2, and c3 , I could not find some explanation for them . Can anyone point to a place where these coefficients are described in detail? The description may explain the 40 number. Best, .Jose -- 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.
Re: [gmx-users] How to parameterize the volume occupied by a protein?
Hi Mark, I decided to write my own script, which computes distances between silica and protein atoms as you suggested. Removing the silica is not trivial because one must remove SiO2 molecules but there is no unique way to partition a silica block into SiO2 molecules. .Jose On Fri, Jun 16, 2017 at 8:54 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You sound like you want a selection of all silica atoms within a distance > of any protein atom, which eg gmx select does. But gmx solvate is built for > the job of removing such atoms - here you are "solvating" 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 onto a silica block (see picture in > > https://goo.gl/ZS9xVm). > > > > Now I need to remove the silica atoms overlapping the protein. This > > requires parameterization of the volume occupied by the protein in a way > > that will let me query whether a point in space 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/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.
[gmx-users] How to parameterize the volume occupied by a protein?
Dear all, I have superimposed a protein onto a silica block (see picture in https://goo.gl/ZS9xVm). Now I need to remove the silica atoms overlapping the protein. This requires parameterization of the volume occupied by the protein in a way that will let me query whether a point in space 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/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.
[gmx-users] (Newbie) Residue SiO2 for solvation?
Dear Gromacs users, I want to encase this mildly hydrated protein <http://nbviewer.jupyter.org/github/jmborr/confinedBSA/blob/master/simulation/monomer/solvatedBSA/minimize/relax/stripped_system_h0.17.gif> within an amorphous silica cube, so I thought of using gmx solvate. Thus, I need a residue for the SiO2 molecule. The OPLS force field includes non-bonded parameters for SI atom, but no SiO2 "residue". Has anyone gone through this particular problem? Or can anyone give me some pointer as to how create a custom residue starting from, say, a PDB file of the molecule, and 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/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.
Re: [gmx-users] Remove all but N closest water molecules from protein
Hi Mark, The following lines select solvent molecules within some cutoff distance of the protein: close_solvent_atoms = group "SOL" and within 0.5 of group "Protein"; close_solvent_molecules = same resindex as close_solvent_atoms; "strippedSystem" group "Protein" or close_solvent_molecules; It's not exactly what I wanted, butI can select N closest water molecules by tuning the cutoff distance. .Jose On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Or gmx select to make an index group for the nearest waters, and gmx > trjconv to make the subset with the index group. > > Mark > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > joao.m.a.henriq...@gmail.com> > wrote: > > > Hi, > > > > trjorder can reorder the water molecules in each 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 > > stuff on gmx 2016. > > > > Cheers, > > João > > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" <borregu...@gmail.com> wrote: > > > > 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 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.
[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 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.
Re: [gmx-users] Installation woe: fatal error: mpi.h: No such file or directory
Hi Mark, I followed your instructions and had no problem at all with the install. Thanks a lot! .Jose On Tue, Aug 2, 2016 at 7:00 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > That seems a lot more complicated than you should need. First, don't run > the whole script as sudo unless you like re-installing OSes. As the install > guide says, you only need the install stage as sudo. You haven't set the > C++ compiler, either, so that might why it hasn't found mpi.h when > compiling a C++ file. You've managed a whole pile of things that don't need > to be managed if you have a normal installation of OpenMPI - the whole > point of using the wrapper compilers is that they already know where to > find the matching headers and libraries. > > GROMACSDIR=/SNSlocal/sw/gromacs/gromacs-5.1.3 > module load mpi/openmpi-x86_64 > mkdir -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_LIBS=off > > Mark > > On Wed, Aug 3, 2016 at 12:06 AM Jose Borreguero <borregu...@gmail.com> > wrote: > > > 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 > > > > > /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/commandline/cmdlineinit.cpp:56: > > /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/utility/gmxmpi.h:61:17: > > fatal error: mpi.h: No such file or directory > > compilation terminated. > > > > My installation script: > > > > #!/bin/bash > > # To run, issue: > > # $> sudo su - -c /SNSlocal/sw/gromacs/gromacs-5.1.3/myInstall.sh > > > > GROMACSDIR=/SNSlocal/sw/gromacs/gromacs-5.1.3 > > module load mpi/openmpi-x86_64 > > mkdir -p $GROMACSDIR/install > > mkdir -p $GROMACSDIR/build > > cd $GROMACSDIR/build > > > > cmake $GROMACSDIR -DCMAKE_INCLUDE_PATH=/usr/include/openmpi-x86_64 > > -DCMAKE_LIBRARY_PATH=/usr/lib64/openmpi/li\ > > b -DCMAKE_PREFIX_PATH=/usr/lib64/openmpi/bin > > -DCMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc -DGMX_MPI=ON -DG\ > > MX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON > > -DCMAKE_INSTALL_PREFIX=/SNSlocal/sw/gr\ > > omacs/gromacs-5.1.3/install > > > > make -j 24 > > make install > > > > As you see, I have populated variable CMAKE_INCLUDE_PATH > > Furthermore: > > $> locate mpi.h > > $> /usr/include/openmpi-x86_64/mpi.h > > > > This is what I get by grepping the CMakeCache.txt: > > $> grep "openmpi-x86_64" CMakeCache.txt > > > CMakeCache.txt:CMAKE_INCLUDE_PATH:UNINITIALIZED=/usr/include/openmpi-x86_64 > > > > and under CMakeFiles/ directory: > > $> grep -R "openmpi-x86_64" * > > CMakeOutput.log:COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_a8886' '-rdynamic' > '-I' > > '/usr/include/openmpi-x86_64' '-pthread' '-L/usr/lib64/openmpi/lib' > > '-mtune=generic' '-march=x86-64' > > CMakeOutput.log: ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' > 'cmTC_a8886' > > '-rdynamic' '-I' '/usr/include/openmpi-x86_64' '-pthread' > > '-L/usr/lib64/openmpi/lib' '-mtune=generic' '-march=x86-64'] > > > > The last info, the ignore line seems suspicious but I don't know what it > > means. > > I'm stuck here, please any help will be much appreciated. > > > > Best, > > .Jose > > -- > > 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.
[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 /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/commandline/cmdlineinit.cpp:56: /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/utility/gmxmpi.h:61:17: fatal error: mpi.h: No such file or directory compilation terminated. My installation script: #!/bin/bash # To run, issue: # $> sudo su - -c /SNSlocal/sw/gromacs/gromacs-5.1.3/myInstall.sh GROMACSDIR=/SNSlocal/sw/gromacs/gromacs-5.1.3 module load mpi/openmpi-x86_64 mkdir -p $GROMACSDIR/install mkdir -p $GROMACSDIR/build cd $GROMACSDIR/build cmake $GROMACSDIR -DCMAKE_INCLUDE_PATH=/usr/include/openmpi-x86_64 -DCMAKE_LIBRARY_PATH=/usr/lib64/openmpi/li\ b -DCMAKE_PREFIX_PATH=/usr/lib64/openmpi/bin -DCMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc -DGMX_MPI=ON -DG\ MX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/SNSlocal/sw/gr\ omacs/gromacs-5.1.3/install make -j 24 make install As you see, I have populated variable CMAKE_INCLUDE_PATH Furthermore: $> locate mpi.h $> /usr/include/openmpi-x86_64/mpi.h This is what I get by grepping the CMakeCache.txt: $> grep "openmpi-x86_64" CMakeCache.txt CMakeCache.txt:CMAKE_INCLUDE_PATH:UNINITIALIZED=/usr/include/openmpi-x86_64 and under CMakeFiles/ directory: $> grep -R "openmpi-x86_64" * CMakeOutput.log:COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_a8886' '-rdynamic' '-I' '/usr/include/openmpi-x86_64' '-pthread' '-L/usr/lib64/openmpi/lib' '-mtune=generic' '-march=x86-64' CMakeOutput.log: ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_a8886' '-rdynamic' '-I' '/usr/include/openmpi-x86_64' '-pthread' '-L/usr/lib64/openmpi/lib' '-mtune=generic' '-march=x86-64'] The last info, the ignore line seems suspicious but I don't know what it means. I'm stuck here, please any help will be much appreciated. Best, .Jose -- 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.
