date:20151016

[gmx-users] error analysis in gmx wham

2015-10-16 Thread Sepideh Kavousi

Hi,
I am calculating PMF fir a tocopherol in DMPC bilayer. I used the gmx wham
to calculate the error, but I am not sure which method gives me the best
results. Can anyone please help me to choose which error analysis method?
Regards
Sepideh
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Re: [gmx-users] Building a box

2015-10-16 Thread Tsjerk Wassenaar

Hi Thomas,

You can build a box by specifying vector lengths and angles: gmx editconf
-box ... -angles ... . Mind that you don't have full freedom like that, as
the box matrix will be upper triangular and reduced (the projection of a
later vector on a previous may not be larger than half that vector). But
any lattice/box can be rotated and deskewed to meet these criteria.

Hope it helps,

Tsjerk
On Oct 16, 2015 6:41 PM, "thomas knitter"  wrote:

> Hi there,
>
> Is there anyway that I could build a box which has different lengths in all
> directions like that below:
>
>a11  a12   a13
>a21  a22   a23
>a31  a32   a33
>
> Thanks
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[gmx-users] Installation of GROMACS 5.1

2015-10-16 Thread Mikhail Stukan

Dear all,

I am facing the following problem during installation of GROMACS 5.1. After 
successful run of cmake, make and make install the only executable file I have 
in corresponding bin directory is "gmx" (actually gmx5.1single in my case). No 
usual grompp, mdrun etc. From the analysis of make logs it looks like all the 
other files were compiled but not linked.

The cmake string I use is
cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_DOUBLE=OFF 
-DGMX_CPU_ACCELERATION=AVX_256
-DBUILD_SHARED_LIBS=OFF -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=5.1single 
-DGMX_LIBS_SUFFIX=5.1single
-DCMAKE_INSTALL_PREFIX:PATH=/home/mstukan/gmx-5.1single

When I tried to use option
-DGMX_BUILD_MDRUN_ONLY=ON
Required mdrun file was successfully compiled, linked and installed in 
corresponding bin directory. However, all attempts to created full package 
failed up to now.

I have previously installed 4.x.x and 5.0.x versions and never had problems 
similar to this.

Any advice on this issue will be highly appreciated.

Many thanks in advance,

Mikhail


Mikhail Stukan, Ph.D.
Senior Research Scientist
Schlumberger Moscow Research
13, Pudovkina st.
Moscow, 119285
Russia
Tel: +7 495 9358200 ext 24017
Fax: +7 495 9358780
mstu...@slb.com

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[gmx-users] ligand contact map

2015-10-16 Thread Albert


Hello:

I would like to calculate which residues does my ligand contact with 
during the MD simulation. I am just wondering is there any module for 
calculating ligand contact map?


Thank you very much

Albert
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Re: [gmx-users] g_mmpbsa time

2015-10-16 Thread rajendra kumar

You may use -dt as option in g_mmpbsa. For example, -dt 600 or -dt 120 .

On Thursday, September 17, 2015 at 7:41:25 AM UTC+2, elham wrote:
>
> Dear users
> i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps
> for binding free energy computations by g_mmpbsa method in gromacs, my 
> computations took a long time
> is it correct?
> can i change my simulation time in *mdp* file for *tpr* production for  
> using in g_mmpbsa calculations or it s equal to  the time of my 
> siulation ???
> regards
>
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Re: [gmx-users] Installation of GROMACS 5.1

2015-10-16 Thread Mirco Wahab


On 16.10.2015 09:14, Mikhail Stukan wrote:

Dear all,

I am facing the following problem during installation of GROMACS 5.1. After successful 
run of cmake, make and make install the only executable file I have in corresponding bin 
directory is "gmx" (actually gmx5.1single in my case). No usual grompp, mdrun 
etc. From the analysis of make logs it looks like all the other files were compiled but 
not linked.

The cmake string I use is
cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_DOUBLE=OFF 
-DGMX_CPU_ACCELERATION=AVX_256
-DBUILD_SHARED_LIBS=OFF -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=5.1single 
-DGMX_LIBS_SUFFIX=5.1single
-DCMAKE_INSTALL_PREFIX:PATH=/home/mstukan/gmx-5.1single

When I tried to use option
-DGMX_BUILD_MDRUN_ONLY=ON
Required mdrun file was successfully compiled, linked and installed in 
corresponding bin directory. However, all attempts to created full package 
failed up to now.

I have previously installed 4.x.x and 5.0.x versions and never had problems 
similar to this.


Since Aug 2015:
http://permalink.gmane.org/gmane.science.biology.gromacs.announce/39

" no more symlinks from grompp to gmx grompp, etc. (as forecast in 
GROMACS 5) "


So, "mdrun" is "gmx mdrun" etc.

M.


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Re: [gmx-users] ligand contact map

2015-10-16 Thread Teemu Murtola

Hi,

At least for some definitions of contacts, you can get what you want with
suitable use of gmx select. With a suitable selection that selects residues
that you consider to be in contact, and depending on what you want, -on,
-om, or -of should give you something useful.

Best regards,
Teemu

On Fri, Oct 16, 2015, 09:05 Albert  wrote:

> Hello:
>
> I would like to calculate which residues does my ligand contact with
> during the MD simulation. I am just wondering is there any module for
> calculating ligand contact map?
>
> Thank you very much
>
> Albert
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[gmx-users] cluster analysis on HREX results

2015-10-16 Thread Shyno Mathew

Dear all,

1. For the cluster analysis, I am using the gromos method with cutoff 0.25
nm.
With this cutoff I got 201 structures for the lowest temperature for
trajectories that are continuous in time (after using demux.pl)
The rmsd ranges from 0.073 to 1.55nm.

If I reduce the cutoff to 0.1 nm I will get 1919 structures, which is very
close to the total number of frames, 2001 in the .xtc file. This doesn't
make sense as I am getting one structure for each frame. Here 1 frame
corresponds to 0.01 ns

My question, with the cluster analysis, do you fix the value of cutoff or
you change cutoff to get a certain number of structures?

Following is the syntax I used:
 g_cluster_mpi -s PRO0.gro -f redPRO0.xtc -method gromos -sz clustsize0.xvg
-o clusters0.xpm -g cluster0.log -clid clusidovertime0.xvg -cl out0.pdb
-cutoff 0.25

2. For replica exchange,is it better to do the cluster analysis on
trajectories that are continuous in ensemble or trajectories that are
continuous in time (after using demux.pl)
I tried both ways:
For replica 0 (for trajectories that are continuous in ensemble, at lowest
temperature 300 K), I got two structures with cutoff 0.25
For replica0 (for trajectories that are continuous in time), I got 201
structures with cutoff 0.25

Thanks in advance for your help.

thanks,
Shyno
-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
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[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

2015-10-16 Thread Ana Marija

HI,

I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
using this gromacs.
But I am getting this error:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
_pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51 2015]
PE RANK 0 exit signal Segmentation fault

But when I use imput files generated with gromacs 4.5.5  with gromacs 4.6.7
it works.
I don't understand this -- is gromacs-4.6.7 is a flaw version that can not
generate input files?
And it not what I am doing wrong in my installation?

I installed 4.6.7  via following process:

module swap PrgEnv-cray PrgEnv-gnu
module load fftw/3.3.4.0
module load cray-mpich/7.0.5
module load gsl/1.15
module load cmake
#in /lustre/beagle2/ams/new/gromacs make directory lib2

mkdir lib2

ams@login1:/lustre/beagle2/ams/lib2>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
ams@login1:/lustre/beagle2/ams/lib2>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a

tar zxvf plumed-2.2.0.tgz
cd plumed-2.2.0

./configure CC=cc CXX=CC F77=ftn
LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
--prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
--disable-basic-warnings --disable-openmp

###Makefile.conf should look like this, if not please delete all
extra stuff before proceeding to make step
CC=cc
FC=gfortran
LDF90=gfortran
CFLAGS=-g -O2 -fPIC
CXX=CC
CXXFLAGS=-O -fPIC
CXXFLAGS_NOOPENMP=-O -fPIC
CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
-DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
-D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
-D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
-D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
-D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
-D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
LDFLAGS=
DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/new/gromacs/lib2
LIBS=-ldl
SOEXT=
LD=CC
LDSO=CC -shared
GCCDEP=CC
prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
program_transform_name=s,x,x,
program_can_run_mpi=yes
program_can_run=yes
LD_RO=ld -r -o
exec_prefix=${prefix}
bindir=${exec_prefix}/bin
libdir=${exec_prefix}/lib
includedir=${prefix}/include
datarootdir=${prefix}/share
datadir=${datarootdir}
docdir=${datarootdir}/doc/plumed
htmldir=${docdir}
program_name=plumed
###

make
make install

export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH

#1. Make a directory for modulefiles (e.g. /lustre/beagle2/ams/modulefiles/)
#2. Copy file
/lustre/beagle2/ams/groplu/plumed-2.1.1/lib/plumed/src/lib/modulefile into
/lustre/beagle2/ams/modulefiles/plumed/2.1.1/
#3. type "module use /lustre/beagle2/ams/modulefiles/"
#4. type "module load plumed/2.1.1"

export PATH=/lustre/beagle2/ams/groplu/plumed-2.1.1/bin:$PATH
module use /lustre/beagle2/ams/modulefiles/
module load plumed/2.1.1

### instal gromacs 4.6.7
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
tar zxvf gromacs-4.6.7.tar.gz
cd gromacs-4.6.7/
ams@login1:/lustre/beagle2/ams/groplu/gromacs-4.6.7>plumed-patch -p --static


PLUMED patching tool

1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2

Choose the best matching code/version:3

mkdir build
cd build


export BUILD_WITH_INSTALL_RPATH=TRUE
export INSTALL_RPATH=""
export SKIP_BUILD_RPATH=TRUE
export
CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/groplu/lib:$CMAKE_LIBRARY_PATH"

#in /lustre/beagle2/ams/groplu make directory lib

ams@login1:/lustre/beagle2/ams/lib>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
ams@login1:/lustre/beagle2/ams/lib>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a


cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
-DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
-DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
-DGMX_DOUBLE=OFF

Re: [gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

2015-10-16 Thread Mark Abraham

Hi,

4.6.7 is fine, but you are probably having trouble with the fact that your
login node is a different kind of machine from your compute node, and
you'll need to consult your local docs for how to set up the cross
compilation environment to work correctly (and then how to tell PLUMED
about it). There's generally no reason to want to run grompp on the compute
nodes, nor mdrun on the login nodes, but if I'm right then the way they've
designed your infrastructure requires you to know what you'll plan to do
later. 4.5.5 doesn't complain because that version is too old for the
GROMACS build system to know the difference between your nodes, so it can
do nothing wrong (but also nothing good).

Mark

On Fri, Oct 16, 2015 at 5:21 PM Ana Marija 
wrote:

> HI,
>
> I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
> using this gromacs.
> But I am getting this error:
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> _pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51 2015]
> PE RANK 0 exit signal Segmentation fault
>
> But when I use imput files generated with gromacs 4.5.5  with gromacs 4.6.7
> it works.
> I don't understand this -- is gromacs-4.6.7 is a flaw version that can not
> generate input files?
> And it not what I am doing wrong in my installation?
>
> I installed 4.6.7  via following process:
>
> module swap PrgEnv-cray PrgEnv-gnu
> module load fftw/3.3.4.0
> module load cray-mpich/7.0.5
> module load gsl/1.15
> module load cmake
> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>
> mkdir lib2
>
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>
> tar zxvf plumed-2.2.0.tgz
> cd plumed-2.2.0
>
> ./configure CC=cc CXX=CC F77=ftn
> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> --disable-basic-warnings --disable-openmp
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> CC=cc
> FC=gfortran
> LDF90=gfortran
> CFLAGS=-g -O2 -fPIC
> CXX=CC
> CXXFLAGS=-O -fPIC
> CXXFLAGS_NOOPENMP=-O -fPIC
> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> LDFLAGS=
> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/new/gromacs/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
> program_transform_name=s,x,x,
> program_can_run_mpi=yes
> program_can_run=yes
> LD_RO=ld -r -o
> exec_prefix=${prefix}
> bindir=${exec_prefix}/bin
> libdir=${exec_prefix}/lib
> includedir=${prefix}/include
> datarootdir=${prefix}/share
> datadir=${datarootdir}
> docdir=${datarootdir}/doc/plumed
> htmldir=${docdir}
> program_name=plumed
> ###
>
> make
> make install
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/modulefiles/)
> #2. Copy file
> /lustre/beagle2/ams/groplu/plumed-2.1.1/lib/plumed/src/lib/modulefile into
> /lustre/beagle2/ams/modulefiles/plumed/2.1.1/
> #3. type "module use /lustre/beagle2/ams/modulefiles/"
> #4. type "module load plumed/2.1.1"
>
> export PATH=/lustre/beagle2/ams/groplu/plumed-2.1.1/bin:$PATH
> module use /lustre/beagle2/ams/modulefiles/
> module load plumed/2.1.1
>
> ### instal gromacs 4.6.7
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> tar zxvf gromacs-4.6.7.tar.gz
> cd gromacs-4.6.7/
> ams@login1:/lustre/beagle2/ams/groplu/gromacs-4.6.7>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2
>
> Choose the best matching code/version:3
>
> mkdir build
> cd build
>
>
> export BUILD_WITH_INSTALL_RPATH=TRUE
> export INSTALL_RPATH=""
> export SKIP_BUILD_RPATH=TRUE
> export
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/groplu/lib:$CMAKE_LIBRARY_PATH"
>
> #in /lustre/beagle2/ams/groplu make directory lib
>
> ams@login1:/lustre/beagle2/ams/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib>ln -s
>

Re: [gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

2015-10-16 Thread Mark Abraham

Hi,

Please keep the discussion on the list. Someone else may have this problem
some time.

On Fri, Oct 16, 2015 at 5:51 PM Ana Marija 
wrote:

> HI Mark,
>
> but I do use cross compiler flags like: -DCMAKE_CXX_COMPILER=CC
> -DCMAKE_C_COMPILER=cc
> because yes I want to run it on compute nodes.
>

You still need the right modules loaded at cmake, build and run time. You
should ask your sysadmins to help you install a normal gromacs 4.6.7, and
then steal their ideas ;-)


> Also I'm using cross compiler flags for plumed. Is there is another thing
> I can change there?
>

No idea, but you should ask them. :-)


> Also you are saying that I shouldn't use imput files generated with 4.5.5
> with 4.6.7?
>

You should prefer to use grompp that matches the mdrun, and you should not
run grompp on the compute nodes at all! That's why grompp produces a fully
portable standalone .tpr.

Mark


>
> Thanks
> Ana
>
> On Fri, Oct 16, 2015 at 10:45 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> 4.6.7 is fine, but you are probably having trouble with the fact that
>> your login node is a different kind of machine from your compute node, and
>> you'll need to consult your local docs for how to set up the cross
>> compilation environment to work correctly (and then how to tell PLUMED
>> about it). There's generally no reason to want to run grompp on the compute
>> nodes, nor mdrun on the login nodes, but if I'm right then the way they've
>> designed your infrastructure requires you to know what you'll plan to do
>> later. 4.5.5 doesn't complain because that version is too old for the
>> GROMACS build system to know the difference between your nodes, so it can
>> do nothing wrong (but also nothing good).
>>
>> Mark
>>
>> On Fri, Oct 16, 2015 at 5:21 PM Ana Marija 
>> wrote:
>>
>>> HI,
>>>
>>> I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
>>> using this gromacs.
>>> But I am getting this error:
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>>> _pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51
>>> 2015]
>>> PE RANK 0 exit signal Segmentation fault
>>>
>>> But when I use imput files generated with gromacs 4.5.5  with gromacs
>>> 4.6.7
>>> it works.
>>> I don't understand this -- is gromacs-4.6.7 is a flaw version that can
>>> not
>>> generate input files?
>>> And it not what I am doing wrong in my installation?
>>>
>>> I installed 4.6.7  via following process:
>>>
>>> module swap PrgEnv-cray PrgEnv-gnu
>>> module load fftw/3.3.4.0
>>> module load cray-mpich/7.0.5
>>> module load gsl/1.15
>>> module load cmake
>>> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>>>
>>> mkdir lib2
>>>
>>> ams@login1:/lustre/beagle2/ams/lib2>ln -s
>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>> ams@login1:/lustre/beagle2/ams/lib2>ln -s
>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>>
>>> tar zxvf plumed-2.2.0.tgz
>>> cd plumed-2.2.0
>>>
>>> ./configure CC=cc CXX=CC F77=ftn
>>> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
>>> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
>>> --disable-basic-warnings --disable-openmp
>>>
>>> ###Makefile.conf should look like this, if not please delete all
>>> extra stuff before proceeding to make step
>>> CC=cc
>>> FC=gfortran
>>> LDF90=gfortran
>>> CFLAGS=-g -O2 -fPIC
>>> CXX=CC
>>> CXXFLAGS=-O -fPIC
>>> CXXFLAGS_NOOPENMP=-O -fPIC
>>> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
>>> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
>>> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>>> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
>>> -DHAVE_INTTYPES_H=1
>>> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
>>> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
>>> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
>>> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
>>> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
>>> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
>>> LDFLAGS=
>>> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/new/gromacs/lib2
>>> LIBS=-ldl
>>> SOEXT=
>>> LD=CC
>>> LDSO=CC -shared
>>> GCCDEP=CC
>>> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
>>> program_transform_name=s,x,x,
>>> program_can_run_mpi=yes
>>> program_can_run=yes
>>> LD_RO=ld -r -o
>>> exec_prefix=${prefix}
>>> bindir=${exec_prefix}/bin
>>> libdir=${exec_prefix}/lib
>>> includedir=${prefix}/include
>>> datarootdir=${prefix}/share
>>> datadir=${datarootdir}
>>> docdir=${datarootdir}/doc/plumed
>>> htmldir=${docdir}
>>> program_name=plumed
>>> ###
>>>
>>> make
>>> make install
>>>
>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>
>>> #1. Make a directory for modulefiles (e.g.
>>>

Re: [gmx-users] Dynamic Cross Correlation

2015-10-16 Thread Naba

Hi,

you can compute dynamic cross correlation using Bio3D package within R.
Follow this link: http://thegrantlab.org/bio3d/tutorials/trajectory-analysis

Regards,
Naba

On Sat, Oct 17, 2015 at 4:14 AM, ANAND AMITKUMAR Dharia <
adha...@berkeley.edu> wrote:

> Hello,
>
> Is there any method in GROMACS to compute dynamic cross correlation between
> different molecules. If not defined in GROMACS, what are methods people
> take to compute coupling from the trajectory data.
>
> Thanks,
> Anand Dharia
> --
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Building a box

2015-10-16 Thread thomas knitter

Hi there,

Is there anyway that I could build a box which has different lengths in all
directions like that below:

   a11  a12   a13
   a21  a22   a23
   a31  a32   a33

Thanks
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] error analysis in gmx wham

Re: [gmx-users] Building a box

[gmx-users] Installation of GROMACS 5.1

[gmx-users] ligand contact map

Re: [gmx-users] g_mmpbsa time

Re: [gmx-users] Installation of GROMACS 5.1

Re: [gmx-users] ligand contact map

[gmx-users] cluster analysis on HREX results

[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

Re: [gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

Re: [gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

Re: [gmx-users] Dynamic Cross Correlation

[gmx-users] Building a box

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