[gmx-users] Gromacs in Mac OS 10.11 (el capitan) (Eudes Fileti) (SOLVED)
Eudes Fileti
fileti at gmail.com
Sun Jun 5 04:39:34 CEST 2016
Hello gmx-users,
I managed to install the gromacs 5.1.2 in El capitan simply deleting the
option "-DREGRESSIONTEST_DOWNLOAD=ON" from cmake command. So, the script I
used for dirty installation was:
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
bests
eef
------------------------------
>
> Message: 4
> Date: Fri, 3 Jun 2016 17:36:17 -0300
> From: Eudes Fileti <fileti at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Gromacs in Mac OS 10.11 (el capitan)
> Message-ID:
> <CAHC5Q=h1FSKy3Z6XGD2hfML8_RxBq4wyvHkW+tZsZVifz5-U=
> g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> I'm following the standard script below for Gromacs installation, as usual
> I do:
>
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> make
> make check
> sudo make install
>
>
> But this time I'm getting a strange error after "cmake" command:
>
> fileti:~/Downloads/gromacs-5.1.2/build$make
> [ 1%] Built target fftwBuild
> make[2]: *** No rule to make target
>
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Accelerate.framework',
> needed by `lib/libgromacs.1.2.0.dylib'. Stop.
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
>
> Someone also had any problems withMac OS 10.11 (el capitan) to INSTALLING
> gromacs?
>
> Any suggestion?
>
> Bests
> eef
> _______________________________________
> Eudes Eterno Fileti
> Instituto de Ci?ncia e Tecnologia da UNIFESP
> Av. Cesar Lattes, 1201, Eug?nio de Mello, SP, 12247-014
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 3 Jun 2016 22:49:01 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] error installing trj_cavity with gromacs
> Message-ID:
> <CABzE1Sh6=XdvPewZebk970LGGboL=
> zUwJomxXL2S9BeCDHYfEw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Williams,
>
> It looks like you didn't set the Gromacs include directory. What
> command/procedure did you use to compile?
>
> Cheers,
>
> Tsjerk
> On Jun 3, 2016 21:25, "Williams Miranda" <williams.miranda at ucalgary.ca>
> wrote:
>
> > Dear GROMACS users
> > I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation.
> > But I am getting this error:
> >
> >
> > src/AtomReaderGromacs.cpp:13:19: fatal error: xtcio.h: No such file or
> > directory
> >
> >
> > Actually, the AtomReaderGromacs.cpp includes the following files:
> >
> > include "xtcio.h"
> > include "trajana.h"
> > include "statutil.h"
> > include "typedefs.h"
> > include "smalloc.h"
> > include "copyrite.h"
> > include "tpxio.h"
> > include "names.h"
> > include "gmx_random.h"
> > include "gmx_ana.h"
> > include "filenm.h"
> > include "macros.h"
> > include "pbc.h"
> > include "vec.h"
> > include "xvgr.h"
> > include "pdb2top.h"
> >
> > However, only typedefs.h is found in my GROMACS library. What could I do
> > to fix this problem?
> > Regards
> >
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 3 Jun 2016 17:03:07 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gen-pairs
> Message-ID: <5b71a808-dbf7-14a2-eb36-7773595ba3e6 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 6/3/16 8:49 AM, Alexander Alexander wrote:
> > Dear Gromacs user,
> >
> > Surprisingly I am wondering why I have no warning while I assigned "NO"
> for
> > the "gen-pairs" in [ default ] section of my .top file, although I have
> no
> > pair type neither in my .top file nor in ffnonbonded.itp for these atoms?
> >
>
> Pairs are 1-4 (intramolecular) interactions. You have two atom types that
> are
> not bonded, so there are no pair interactions.
>
> -Justin
>
> > I am referring to this statement in gromacs-manual: "When gen-pairs is
> set
> > to ?no,? grompp will give a warning for each pair type for which no
> > parameters are given".
> >
> > My system is a pure transition metal solid that it's topol file comes
> below:
> >
> > topol.top
> > -------------------------
> > ; topol file for A3B
> > ; force field parameters in below
> > [ Defaults ]
> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> > 1 3 no
> > 0.5 0.5
> >
> > [ atomtypes ]
> > ; name mass charge ptype sigma epsilon
> > A 32.00 0.21 A 2.27357e-01
> > 25.1
> > B 6.700 -0.63 A 1.714534e-01
> 4.4
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > A 1
> > [ atoms ]
> > ; nr at type resnr residue atom name cgnr charge
> mass
> > 1 A 1 A A
> > 1 0.21 32.00
> >
> > [ position_restraints ]
> > ; ai funct fcx fcy fcz
> > 1 1 2000 2000 2000
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > B 1
> > [ atoms ]
> > ; nr at type resnr residue atom name cgnr charge
> mass
> > 1 B 1 B B
> > 1 -0.630 6.70
> >
> > [ position_restraints ]
> > ; ai funct fcx fcy fcz
> > 1 1 2000 2000 2000
> >
> > [ system ]
> > ; Name
> > A3B
> >
> > [ molecules ]
> > ;mol_name number
> > A 14400
> > B 4800
> > -----------------------------------------------------
> >
>
> --
> ==================================================
>
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 146, Issue 20
> ******************************************************
>
More information about the gromacs.org_gmx-users
mailing list