Dear community.
Thank you for your help. After doing "./configure" without problems, the
system showed ERROR again after "make".Here, I put the steps that I
followed, what is my error?. Please help me with your advices. By the way...
I made a mistake, I am using Rocks cluster 5.4.
root@bioinfocluster gromacs-4.5.4]# mpi-selector-menu
Current system default: openmpi-1.4-gcc-x86_64
Current user default: <none>
"u" and "s" modifiers can be added to numeric and "U"
commands to specify "user" or "system-wide".
1. openmpi-1.4-gcc-i386
2. openmpi-1.4-gcc-x86_64
3. rocks-openmpi-1.4.1
4. sun-ct-8.2.1-i386
5. sun-ct-8.2.1-x86_64
U. Unset default
Q. Quit
Selection (1-5[us], U[us], Q):
1. export CPPFLAGS="-I/opt/rocks/include"
2. export LDFLAGS="-L/opt/rocks/lib"
3.
4. ./configure --enable-mpi --prefix=/share/apps/opt/gromacs
*
*
*Until this point, I did not have errors, then...*
# make
....
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/share/apps/src/gromacs-4.5.4/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/share/apps/src/gromacs-4.5.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/share/apps/src/gromacs-4.5.4/src'
make: *** [all-recursive] Error 1
*Thanks in advance.
Miguel.*
2011/4/11 <gmx-users-requ...@gromacs.org>
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> Today's Topics:
>
> 1. Re: comm-grps for a membrane-protein-ligand system
> (Justin A. Lemkul)
> 2. Re: How to install GROMACS in Rocks Cluster 4.5.4 : ERROR
> (Justin A. Lemkul)
> 3. Re: g_hbond (Erik Marklund)
> 4. Pressure coupling problem (Fabian Casteblanco)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Apr 2011 13:58:24 -0400
> From: "Justin A. Lemkul" <jalem...@vt.edu>
> Subject: Re: [gmx-users] comm-grps for a membrane-protein-ligand
> system
> To: "Gromacs Users' List" <gmx-users@gromacs.org>
> Message-ID: <4da34140.6040...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Peter C. Lai wrote:
> > Ok thanks
> >
> > My primary concern is to cancel membrane-protein drift - the protein
> > getting pushed to one side of the membrane box (also it's important for
> > me to have the protein stay centered in the box too). I have not seen
>
> There is no "center" to a periodic system. Molecules diffuse, there's no
> way
> around it. If you try to apply some biasing force to fit some
> visualization
> convenience, you're potentially damaging the simulation's integrity.
>
> > stability issues otherwise with COM turned on in the case of the unbound
> > protein and the membrane as separate COM groups. The only instability
> > I have encountered thus far is LINCS crashing due to too much forces if
> > I set the restraint forces too high (like 100000 kJ/mol), but I've
> resigned
> > myself to the fact that the residual RMS drift appears acceptable at the
> end
> > of membrane/solvent equilibration runs if I drop it down to 10000 kJ/mol
> > during NPT equilibration).
>
> Position restraints do not fix anything in place, they merely provide an
> energy
> barrier that penalizes change. If your goal is simply to obtain a
> reasonably
> equilibrated system, then there is no need for a force constant above about
> 1000, otherwise you may be overtly influencing the ability of your system
> to
> respond to change.
>
> -Justin
>
> >
> > On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote:
> >>
> >> Peter C. Lai wrote:
> >>> Should I couple a ligand associated with a membrane protein to the same
> >>> COM group as the Protein_POPC group? It makes sense to me that would be
> the
> >>> case since if we are investigating the interaction between
> protein+membrane
> >>> and ligand we want to have the same COM correction vector applied to
> both
> >>> relative to SOL_Ions but I just wanted to make sure...
> >>>
> >> If specifying multiple groups for COM motion removal, yes, the intuitive
> >> solution is to group the ligand with the protein (since they're
> physically
> >> bound, presumably). The general complication is whether or not multiple
> COM
> >> groups are necessary - if the protein protrudes out into the solvent in
> any
> >> substantial way, you could have instability when the solvent and
> >> protein/membrane COMs get re-set. I have seen this before in the case
> of a
> >> protein in water with separate COM groups (which is not appropriate, for
> the
> >> record). Membrane systems are somewhat more complicated because they
> form
> >> interfaces that can slide, but if the protein somehow affects this
> behavior,
> >> well, I don't know that there's a trivial solution other than "comm_grps
> =
> >> System" to avoid possible instability. If you're interested in
> >> diffusion-related properties, on the other hand, that may not be
> appropriate.
> >> Plenty to think about, but again, probably no "easy" solution.
> >>
> >> -Justin
> >>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Apr 2011 14:01:58 -0400
> From: "Justin A. Lemkul" <jalem...@vt.edu>
> Subject: Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4
> : ERROR
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Message-ID: <4da34216.9050...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Miguel Quiliano Meza wrote:
> > Dear community.
> >
> > I have been trying to install gromacs 4.5.4 in my rocks cluster version
> > 5.4 but unfortunately the system showed "configure: error: Cannot find
> > fftw3 library" after launch the ./configure (you can see below)
> >
> > Really I do not understand because I did before this:
> >
> > # export LDFLAGS="-L/opt/rocks/lib"
> > # export CPPFLAGS="-I/opt/rocks/include"
> >
> > # ./configure --enable-mpi --disable-float
> > --prefix=/share/apps/opt/gromacs
> >
> > configure: error: Cannot find fftw3 library
>
> You have a precision mismatch. By using --disable-float you are trying to
> install Gromacs in double precision (which for most applications is not
> necessary and results in some performance loss). Thus, you need FFTW in
> double
> precision as well. You probably compiled FFTW in single precision, thus
> the
> libraries are named libfftw3f, not libfftw3.
>
> -Justin
>
> >
> > I would be very grateful if someone could help me or give me advices. By
> > the way... I am trying to reproduce the steps posted in
> >
> http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/
> > for
> >
> >
> > "compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference
> > Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0"
> >
> >
> > and the option "--disable-float" is not clear for me.
> >
> >
> > Thank you in advance.
> >
> > Miguel Quiliano.
> >
> > P.S I attach the error
> >
> >
> > # ./configure --enable-mpi --disable-float
> --prefix=/share/apps/opt/gromacs
> > checking build system type... x86_64-unknown-linux-gnu
> > checking host system type... x86_64-unknown-linux-gnu
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... yes
> > checking for a thread-safe mkdir -p... /bin/mkdir -p
> > checking for gawk... gawk
> > checking whether make sets $(MAKE)... yes
> > checking how to create a ustar tar archive... gnutar
> > checking for cc... cc
> > checking for C compiler default output file name... a.out
> > checking whether the C compiler works... yes
> > checking whether we are cross compiling... no
> > checking for suffix of executables...
> > checking for suffix of object files... o
> > checking whether we are using the GNU C compiler... yes
> > checking whether cc accepts -g... yes
> > checking for cc option to accept ISO C89... none needed
> > checking for style of include used by make... GNU
> > checking dependency style of cc... gcc3
> > checking dependency style of cc... gcc3
> > checking for mpxlc... no
> > checking for mpicc... mpicc
> > checking whether the MPI cc command works... yes
> > checking for MPI_IN_PLACE in collective operations... yes
> > checking for catamount... no
> > checking how to run the C preprocessor... mpicc -E
> > checking for grep that handles long lines and -e... /bin/grep
> > checking for egrep... /bin/grep -E
> > checking whether ln -s works... yes
> > checking whether mpicc accepts -O3... yes
> > checking whether mpicc accepts -msse2... yes
> > checking whether mpicc accepts -funroll-all-loops... yes
> > checking whether mpicc accepts -std=gnu99... yes
> > checking whether mpicc accepts -fexcess-precision=fast... no
> > checking whether mpicc accepts -O3 -fomit-frame-pointer
> > -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
> > -std=gnu99... yes
> > checking whether byte ordering is bigendian... no
> > checking that size_t can hold pointers... yes
> > checking for SIGUSR1... yes
> > checking for pipes... yes
> > checking floating-point format... IEEE754 (little-endian byte and word
> > order)
> > checking whether ln -s works... yes
> > checking whether make sets $(MAKE)... (cached) yes
> > checking for a sed that does not truncate output... /bin/sed
> > checking for ld used by mpicc... /usr/bin/ld
> > checking if the linker (/usr/bin/ld) is GNU ld... yes
> > checking for /usr/bin/ld option to reload object files... -r
> > checking for BSD-compatible nm... /usr/bin/nm -B
> > checking how to recognise dependent libraries... pass_all
> > checking dlfcn.h usability... yes
> > checking dlfcn.h presence... yes
> > checking for dlfcn.h... yes
> > checking whether we are using the GNU C++ compiler... yes
> > checking whether mpicc accepts -g... yes
> > checking dependency style of mpicc... gcc3
> > checking how to run the C++ preprocessor... mpicc -E
> > checking the maximum length of command line arguments... 32768
> > checking command to parse /usr/bin/nm -B output from mpicc object...
> failed
> > checking for objdir... .libs
> > checking for ar... ar
> > checking for ranlib... ranlib
> > checking for strip... strip
> > checking if mpicc supports -fno-rtti -fno-exceptions... no
> > checking for mpicc option to produce PIC... -fPIC
> > checking if mpicc PIC flag -fPIC works... yes
> > checking if mpicc static flag -static works... no
> > checking if mpicc supports -c -o file.o... yes
> > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
> > shared libraries... yes
> > checking whether -lc should be explicitly linked in... no
> > checking dynamic linker characteristics... GNU/Linux ld.so
> > checking how to hardcode library paths into programs... immediate
> > checking whether stripping libraries is possible... yes
> > checking for shl_load... no
> > checking for shl_load in -ldld... no
> > checking for dlopen... yes
> > checking whether a program can dlopen itself... yes
> > checking whether a statically linked program can dlopen itself... yes
> > checking if libtool supports shared libraries... yes
> > checking whether to build shared libraries... yes
> > checking whether to build static libraries... yes
> > configure: creating libtool
> > appending configuration tag "CXX" to libtool
> > checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64
> > checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
> > shared libraries... yes
> > checking for mpicc option to produce PIC... -fPIC
> > checking if mpicc PIC flag -fPIC works... yes
> > checking if mpicc static flag -static works... no
> > checking if mpicc supports -c -o file.o... yes
> > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
> > shared libraries... yes
> > checking dynamic linker characteristics... GNU/Linux ld.so
> > checking how to hardcode library paths into programs... immediate
> > appending configuration tag "F77" to libtool
> > checking for special C compiler options needed for large files... no
> > checking for _FILE_OFFSET_BITS value needed for large files... no
> > checking for _LARGEFILE_SOURCE value needed for large files... no
> > checking for sqrt in -lm... yes
> > checking for fftw3.h... yes
> > checking for main in -lfftw3... no
> > configure: error: Cannot find fftw3 library
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Apr 2011 21:32:13 +0200
> From: Erik Marklund <er...@xray.bmc.uu.se>
> Subject: Re: [gmx-users] g_hbond
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Message-ID: <4da3573d.80...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Try the -contact option.
>
> Erik
>
>
> Nilesh Dhumal skrev 2011-04-11 17.12:
> > Is there any way to specify clorin and florin atoms as a receptor.
> >
> > Nilesh
> >
> > On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
> >> Nilesh Dhumal wrote:
> >>
> >>> Hello,
> >>>
> >>>
> >>> I am trying to calculate number of hydrogen bond (O-H---CL)in my
> >>> system.
> >>>
> >>> I use the following command
> >>>
> >>>
> >>>
> >>> g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num
> >>>
> >>>
> >>> Output file hbnum.xvg shows zero number of hydorgen bond.
> >>>
> >>>
> >>> Can you tell me why its showing zero no.
> >>>
> >>>
> >>> A strong peak is found in rdf between H and CL at 2.0 A.
> >>>
> >>>
> >> Chlorine is not considered a receptor in g_hbond.
> >>
> >>
> >> -Justin
> >>
> >>
> >>> I am using Gromacs 4.0.7 version.
> >>>
> >>>
> >>>
> >>>
> >>> Nilesh
> >>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> ========================================
> >>
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >>
> >> ========================================
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
> Read
> >> http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >>
> >
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> er...@xray.bmc.uu.se http://folding.bmc.uu.se/
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 11 Apr 2011 16:55:16 -0400
> From: Fabian Casteblanco <fabian.castebla...@gmail.com>
> Subject: [gmx-users] Pressure coupling problem
> To: gmx-users@gromacs.org
> Message-ID: <BANLkTikp48HDYw63W7vk8Tc=+tsjxqx...@mail.gmail.com>
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>
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