[gmx-users] Fwd: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0

[bharat gupta]

Hi,

I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-

Error:

[root@cluster gromacs-4.5.7]# make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure  --enable-mpi
LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include  --no-create
--no-recursion
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
./configure: line 2050: syntax error near unexpected token `tar-ustar'
./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)'
make: *** [config.status] Error 2


I have another query regarding the gromacs that comes with the Rocks
cluster distribution. The mdrun of that gromacs has been complied without
mpi option. How can I recomplie with mpi option. As I need the .configure
file which is not there in the installed gromacs folder of the rocks
cluster ...


Thanks in advance for help




Regards

Bharat
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[gmx-users] Fwd: Using gromacs on Rocks cluster

[bharat gupta]

Hi,

I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32 processors (cpu). But while running the nvt equilibration step, it uses
only 1 cpu and the others remain idle. I have complied the Gromacs using
enable-mpi option. How can make the mdrun use all the 32 processors ??

--
Bharat
-- 
gmx-users mailing listgmx-users@gromacs.org
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* Please search the archive at 
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Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mark Abraham]

For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
this problem. Run make a second time and it will work.

Mark

On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com wrote:
 Thanks Wahab
 I followed your instruction and added  #define HAVE_SYS_TIME_H

 at the very top of the file gmxlib/thread_mpi/impl.h.
 Then again in make command I got following errors.
 [ 53%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
 [ 53%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
 [ 53%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
 [ 53%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
 [ 53%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
 [ 55%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
 [ 56%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
 [ 56%] Building C object
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
 make[2]: *** No rule to make target
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
 needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
 CMakeFiles/Makefile2:1238: recipe for target
 `src/gmxlib/CMakeFiles/gmx.dir/all' failed
 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
 Makefile:146: recipe for target `all' failed
 make: *** [all] Error 2

 Please help me to compile gromacs 4.6.3 on cygwin

 Shahid Nayeem


 On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab 
 mirco.wa...@chemie.tu-freiberg.de wrote:

 On 10.09.2013 08:20, shahid nayeem wrote:

 I am installing gromacs -4.6.3 on cygwin with following commands
 tar -xvzf gramcs-4.6.3.tar.gz
 cd gromacs-4.6.3
 mkdir build
 cd build
   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
 It runs fine and write file in build directory.
 when I run make command it gives following error.
 ...

 /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
 impl.h:504:20:
 error: field ‘timer_init’ has incomplete type
   struct timeval timer_init;
  ^
 src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target


 The Gromacs-file gmxlib/thread_mpi/impl.h is missing the
 correct #define for the unixish Cygwin pseudo-os. You can
 add it by inserting

  #define HAVE_SYS_TIME_H

 at the very top of the file gmxlib/thread_mpi/impl.h

 Then the package will probably compile and link, but
 mdrun's thread-mpi (tMPI) will not work on Cygwin
 (didn't work last time I tried).

 So you could do the following: 1) install the Gromacs
 package with normal compilation, and 2) build and
 install the openmpi-version of mdrun (mdrun_mpi).

 (1) cmake-options for package:
 ...
   -DGMX_GPU=OFF \
   -DGMX_PREFER_STATIC_LIBS=ON   \
 ...

 make -j4 install

 (delete all files from the build path)

 (2) cmake options for mdrun_mpi
 ...
   -DGMX_GPU=OFF\
   -DGMX_MPI=ON \
   -DGMX_PREFER_STATIC_LIBS=ON  \
 ...

 make -j4 install-mdrun

 The openmpi-version (mdrun_mpi) runs reasonable on
 Cygwin/64 1.7.25, but not as fast as the native
 windows version (compiled with visual studio 10 or 12).
 The windows-compiled version of 4.6.3 is very robust and
 allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12)
 for unknown reasons). Then, you'll have full gpu support
 under windows.

 Regards

 M.

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks. But when I ran make again I am getting this error
[  0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2
 shahid Nayeem


On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
 this problem. Run make a second time and it will work.

 Mark

 On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com wrote:
  Thanks Wahab
  I followed your instruction and added  #define HAVE_SYS_TIME_H
 
  at the very top of the file gmxlib/thread_mpi/impl.h.
  Then again in make command I got following errors.
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
  make[2]: *** No rule to make target
 
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
  needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
  CMakeFiles/Makefile2:1238: recipe for target
  `src/gmxlib/CMakeFiles/gmx.dir/all' failed
  make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
  Makefile:146: recipe for target `all' failed
  make: *** [all] Error 2
 
  Please help me to compile gromacs 4.6.3 on cygwin
 
  Shahid Nayeem
 
 
  On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab 
  mirco.wa...@chemie.tu-freiberg.de wrote:
 
  On 10.09.2013 08:20, shahid nayeem wrote:
 
  I am installing gromacs -4.6.3 on cygwin with following commands
  tar -xvzf gramcs-4.6.3.tar.gz
  cd gromacs-4.6.3
  mkdir build
  cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
  It runs fine and write file in build directory.
  when I run make command it gives following error.
  ...
 
  /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
  impl.h:504:20:
  error: field ‘timer_init’ has incomplete type
struct timeval timer_init;
   ^
  src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target
 
 
  The Gromacs-file gmxlib/thread_mpi/impl.h is missing the
  correct #define for the unixish Cygwin pseudo-os. You can
  add it by inserting
 
   #define HAVE_SYS_TIME_H
 
  at the very top of the file gmxlib/thread_mpi/impl.h
 
  Then the package will probably compile and link, but
  mdrun's thread-mpi (tMPI) will not work on Cygwin
  (didn't work last time I tried).
 
  So you could do the following: 1) install the Gromacs
  package with normal compilation, and 2) build and
  install the openmpi-version of mdrun (mdrun_mpi).
 
  (1) cmake-options for package:
  ...
-DGMX_GPU=OFF \

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks Mark

$ make
[  0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2

I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Please help me

shahid Nayeem


On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem msnay...@gmail.com wrote:

 Thanks. But when I ran make again I am getting this error
 [  0%] Built target gmxfftw
 make[2]: *** No rule to make target
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
 needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
 CMakeFiles/Makefile2:1238: recipe for target
 `src/gmxlib/CMakeFiles/gmx.dir/all' failed
 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
 Makefile:146: recipe for target `all' failed
 make: *** [all] Error 2
  shahid Nayeem


 On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham 
 mark.j.abra...@gmail.comwrote:

 For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
 this problem. Run make a second time and it will work.

 Mark

 On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com
 wrote:
  Thanks Wahab
  I followed your instruction and added  #define HAVE_SYS_TIME_H
 
  at the very top of the file gmxlib/thread_mpi/impl.h.
  Then again in make command I got following errors.
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
  make[2]: *** No rule to make target
 
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
  needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
  CMakeFiles/Makefile2:1238: recipe for target
  `src/gmxlib/CMakeFiles/gmx.dir/all' failed
  make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
  Makefile:146: recipe for target `all' failed
  make: *** [all] Error 2
 
  Please help me to compile gromacs 4.6.3 on cygwin
 
  Shahid Nayeem
 
 
  On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab 
  mirco.wa...@chemie.tu-freiberg.de wrote:
 
  On 10.09.2013 08:20, shahid nayeem wrote:
 
  I am installing gromacs -4.6.3 on cygwin with following commands
  tar -xvzf gramcs-4.6.3.tar.gz
  cd gromacs-4.6.3
  mkdir build
  cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
  It runs fine and write file in build directory.
  when I run make command it gives following error.
  ...
 
  /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
  impl.h:504:20:
  error: field ‘timer_init’ has incomplete type

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mark Abraham]

Don't know, sorry. None of the devs use Cygwin. I suggest you follow
the normal instructions to install FFTW manually, and then direct
CMake to use it.

Mark

On Wed, Sep 11, 2013 at 9:38 AM, shahid nayeem msnay...@gmail.com wrote:
 Thanks Mark

 $ make
 [  0%] Built target gmxfftw
 make[2]: *** No rule to make target
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
 needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
 CMakeFiles/Makefile2:1238: recipe for target
 `src/gmxlib/CMakeFiles/gmx.dir/all' failed
 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
 Makefile:146: recipe for target `all' failed
 make: *** [all] Error 2

 I checked in folder
 /cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
 , this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
 locate it.
 Please help me

 shahid Nayeem


 On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem msnay...@gmail.com wrote:

 Thanks. But when I ran make again I am getting this error
 [  0%] Built target gmxfftw
 make[2]: *** No rule to make target
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
 needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
 CMakeFiles/Makefile2:1238: recipe for target
 `src/gmxlib/CMakeFiles/gmx.dir/all' failed
 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
 Makefile:146: recipe for target `all' failed
 make: *** [all] Error 2
  shahid Nayeem


 On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham 
 mark.j.abra...@gmail.comwrote:

 For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
 this problem. Run make a second time and it will work.

 Mark

 On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com
 wrote:
  Thanks Wahab
  I followed your instruction and added  #define HAVE_SYS_TIME_H
 
  at the very top of the file gmxlib/thread_mpi/impl.h.
  Then again in make command I got following errors.
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
  [ 53%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
  [ 55%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
  [ 56%] Building C object
 
 src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
  make[2]: *** No rule to make target
 
 `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
  needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
  CMakeFiles/Makefile2:1238: recipe for target
  `src/gmxlib/CMakeFiles/gmx.dir/all' failed
  make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
  Makefile:146: recipe for target `all' failed
  make: *** [all] Error 2
 
  Please help me to compile gromacs 4.6.3 on cygwin
 
  Shahid Nayeem
 
 
  On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab 
  mirco.wa...@chemie.tu-freiberg.de wrote:
 
  On 10.09.2013 08:20, shahid nayeem wrote:
 
  I am installing gromacs -4.6.3 on cygwin with following commands
  tar -xvzf gramcs-4.6.3.tar.gz
  cd gromacs-4.6.3
  mkdir build
  cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON 

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mirco Wahab]

On 11.09.2013 09:38, shahid nayeem wrote:

I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.


Did you 'cmake' with -DGMX_PREFER_STATIC_LIBS=ON ?

BTW, from time to time I installed cygwin (out of curiosity)
and installed gromacs in it. The actual cygwin/64 (gcc 4.8)
combined with gromacs 4.6.3 happened to be the first gromacs
installation on cygwin after many years that is really usable.

I used the fftw3 package that came with cygwin (I didn't
use -DGMX_BUILD_OWN_FFTW=ON) and everything build fine
(you'll need -DGMX_PREFER_STATIC_LIBS=ON). This fftw3 was
build without any optimizations but if you don't need
PME electrostatics, you don't have to care.

If you need PME, then you'll have to download the fftw3
to your cygwin home, build it manually (as Mark proposed)
and install it to /usr/local where gromacs will find it.

Regards

M.

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Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mark Abraham]

On Wed, Sep 11, 2013 at 12:04 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
 On 11.09.2013 09:38, shahid nayeem wrote:

 I checked in folder

 /cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
 , this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
 locate it.


 Did you 'cmake' with -DGMX_PREFER_STATIC_LIBS=ON ?

 BTW, from time to time I installed cygwin (out of curiosity)
 and installed gromacs in it. The actual cygwin/64 (gcc 4.8)
 combined with gromacs 4.6.3 happened to be the first gromacs
 installation on cygwin after many years that is really usable.

4.5.x used to build fine for me out of the box on cygwin, but I'd
never attempt a real calculation with it.

Mark

 I used the fftw3 package that came with cygwin (I didn't
 use -DGMX_BUILD_OWN_FFTW=ON) and everything build fine
 (you'll need -DGMX_PREFER_STATIC_LIBS=ON). This fftw3 was
 build without any optimizations but if you don't need
 PME electrostatics, you don't have to care.

 If you need PME, then you'll have to download the fftw3
 to your cygwin home, build it manually (as Mark proposed)
 and install it to /usr/local where gromacs will find it.


 Regards

 M.

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[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Dear all
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.

[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o
[ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o
[ 15%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
[ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o
[ 16%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o
[ 17%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o
[ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o
In file included from
/cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0:
/cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20:
error: field ‘timer_init’ has incomplete type
 struct timeval timer_init;
^
src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2
 Please help me to install this version of gromacs on cygwin

Shahid
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Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mirco Wahab]

On 10.09.2013 08:20, shahid nayeem wrote:

I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
  cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.
...
/cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20:
error: field ‘timer_init’ has incomplete type
  struct timeval timer_init;
 ^
src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target


The Gromacs-file gmxlib/thread_mpi/impl.h is missing the
correct #define for the unixish Cygwin pseudo-os. You can
add it by inserting

 #define HAVE_SYS_TIME_H

at the very top of the file gmxlib/thread_mpi/impl.h

Then the package will probably compile and link, but
mdrun's thread-mpi (tMPI) will not work on Cygwin
(didn't work last time I tried).

So you could do the following: 1) install the Gromacs
package with normal compilation, and 2) build and
install the openmpi-version of mdrun (mdrun_mpi).

(1) cmake-options for package:
...
  -DGMX_GPU=OFF \
  -DGMX_PREFER_STATIC_LIBS=ON   \
...

make -j4 install

(delete all files from the build path)

(2) cmake options for mdrun_mpi
...
  -DGMX_GPU=OFF\
  -DGMX_MPI=ON \
  -DGMX_PREFER_STATIC_LIBS=ON  \
...

make -j4 install-mdrun

The openmpi-version (mdrun_mpi) runs reasonable on
Cygwin/64 1.7.25, but not as fast as the native
windows version (compiled with visual studio 10 or 12).
The windows-compiled version of 4.6.3 is very robust and
allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12)
for unknown reasons). Then, you'll have full gpu support
under windows.

Regards

M.

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Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[shahid nayeem]

Thanks Wahab
I followed your instruction and added  #define HAVE_SYS_TIME_H

at the very top of the file gmxlib/thread_mpi/impl.h.
Then again in make command I got following errors.
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2

Please help me to compile gromacs 4.6.3 on cygwin

Shahid Nayeem


On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab 
mirco.wa...@chemie.tu-freiberg.de wrote:

 On 10.09.2013 08:20, shahid nayeem wrote:

 I am installing gromacs -4.6.3 on cygwin with following commands
 tar -xvzf gramcs-4.6.3.tar.gz
 cd gromacs-4.6.3
 mkdir build
 cd build
   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
 It runs fine and write file in build directory.
 when I run make command it gives following error.
 ...

 /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
 impl.h:504:20:
 error: field ‘timer_init’ has incomplete type
   struct timeval timer_init;
  ^
 src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target


 The Gromacs-file gmxlib/thread_mpi/impl.h is missing the
 correct #define for the unixish Cygwin pseudo-os. You can
 add it by inserting

  #define HAVE_SYS_TIME_H

 at the very top of the file gmxlib/thread_mpi/impl.h

 Then the package will probably compile and link, but
 mdrun's thread-mpi (tMPI) will not work on Cygwin
 (didn't work last time I tried).

 So you could do the following: 1) install the Gromacs
 package with normal compilation, and 2) build and
 install the openmpi-version of mdrun (mdrun_mpi).

 (1) cmake-options for package:
 ...
   -DGMX_GPU=OFF \
   -DGMX_PREFER_STATIC_LIBS=ON   \
 ...

 make -j4 install

 (delete all files from the build path)

 (2) cmake options for mdrun_mpi
 ...
   -DGMX_GPU=OFF\
   -DGMX_MPI=ON \
   -DGMX_PREFER_STATIC_LIBS=ON  \
 ...

 make -j4 install-mdrun

 The openmpi-version (mdrun_mpi) runs reasonable on
 Cygwin/64 1.7.25, but not as fast as the native
 windows version (compiled with visual studio 10 or 12).
 The windows-compiled version of 4.6.3 is very robust and
 allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12)
 for unknown reasons). Then, you'll have full gpu support
 under windows.

 Regards

 M.

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at http://www.gromacs.org/**
 

[gmx-users] Fwd: Fatal error: number of coordinates in coordinate file (trp-b4ion.pdb, 25093) does not match topology (trp.top, 26684)

[Jonathan Saboury]

Files: http://www.sendspace.com/file/vxcnv3

Commands used: http://pastebin.com/raw.php?i=wPqfuUwc

What I want to do: I just want to run the protein without the ligand in
explicit water. Why is the coordinate file not matching topology?

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topologydoesn't
offer much help in this case. I know the problem is the number of
waters however.

Thanks :)
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Re: [gmx-users] Fwd: Fatal error: number of coordinates in coordinate file (trp-b4ion.pdb, 25093) does not match topology (trp.top, 26684)

[Justin Lemkul]

On 7/29/13 6:30 AM, Jonathan Saboury wrote:

Files: http://www.sendspace.com/file/vxcnv3

Commands used: http://pastebin.com/raw.php?i=wPqfuUwc

What I want to do: I just want to run the protein without the ligand in
explicit water. Why is the coordinate file not matching topology?

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topologydoesn't
offer much help in this case. I know the problem is the number of
waters however.



The problem is not the waters.  Your topology specifies 3221 protein+CA atoms, 
but the coordinate file you're using only has 1630.  The problem is here:


pdb2gmx -ff amber99sb -f protein2.pdb -o trp.pdb -p trp.top -water tip3p -ignh

editconf -bt octahedron -f protein2.pdb -o trp‐b4solv.pdb -d 1.0

You're using protein2.pdb to move forward, after pdb2gmx acted upon it (to 
produce conf.gro) to add hydrogens.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Fwd: Gromac trr analysis, wired interacation

[Mark Abraham]

Please keep GROMACS usage questions on the mailing list. If you need
to share a file, do it via a file sharing service, rather than hoping
an individual will appreciate having it in their inbox unsolicited.

On point, do check out the http://www.gromacs.org/Documentation/FAQs,
where a link to the solution for your issue exists.

Mark


-- Forwarded message --
From: Hasni Arsad hasni.ar...@gmail.com
Date: Wed, Jun 26, 2013 at 3:48 AM
Subject: Gromac trr analysis, wired interacation
To: Mark Abraham mark.j.abra...@gmail.com


Hi Mark,

I am very sorry for sending this question directly to you, I have sent
this question to gmx-user discussion but its may rejected because
containing image file.
I am doing MD for 20ns, image in attachment is a part of trr analysis
using VMD. Thank you for your comment  in advance



Hasni
Penang, Malaysia
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[gmx-users] Fwd: puuling simulations

[Sathish Kumar]

Sir,
   I want to do pulling simulations for membrane protein and gold
nanoparticles. Can you please suggest me some tutorials.
  Thank You
-- 
regards
M.SathishKumar



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regards
M.SathishKumar
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Re: [gmx-users] Fwd: Static compilation of gromacs

[Alexey Shvetsov]

В письме от 15 мая 2013 08:41:14 пользователь Андрей Гончар написал:
 I know, but on target machine there is a gcc compilator version 4.1, and on
 gromacs site they told that this version is broken and 4.5 should used
 instead. So I try to compile it on machine with 4.5 version of gcc
 

You can build gcc on target machine for example. also to simplify build you 
can take a look a http://prefix.gentoo.org for example.

 
 2013/5/15 Alexey Shvetsov ale...@omrb.pnpi.spb.ru
 
  В письме от 15 мая 2013 00:11:49 пользователь Андрей Гончар написал:
   Hi. I'm trying to static compile gromacs from source, everything goes
  
  well,
  
   but when I
   move it to another machine and try to launch mdrun I got a message:
   
   mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open
   shared object file: No such file or directory
   
   I run ./configure with the following options:
   
   ./configure --prefix=$PREF --enable-all-static --with-x=no --enable-mpi
   --without-xml --disable-shared --with-fft=fftw3
   
   The goal is to compile gromacs on one computer and to use it on another.
  
  I
  
   haven't root privileges on another machine so I decided to make a
   statically linked instance of gromacs, copy it to another computer and
  
  use
  
   it from my home directory.
  
  You dont need root privileges to install gromacs for example in
  ${HOME}/usr
  also its good idea to build gromacs on target machine
  --
  Best Regards,
  Alexey 'Alexxy' Shvetsov
  Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
  Gatchina, Russia
  Department of Molecular and Radiation Biophysics
  Gentoo Team Ru
  Gentoo Linux Dev
  mailto:alexx...@gmail.com
  mailto:ale...@gentoo.org
  mailto:ale...@omrb.pnpi.spb.ru
  --
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexx...@gmail.com
mailto:ale...@gentoo.org
mailto:ale...@omrb.pnpi.spb.ru

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Re: [gmx-users] Fwd: Static compilation of gromacs

[Mirco Wahab]

On 15.05.2013 06:41, Андрей Гончар wrote:

I know, but on target machine there is a gcc compilator version 4.1, and on
gromacs site they told that this version is broken and 4.5 should used
instead. So I try to compile it on machine with 4.5 version of gcc


Андрей, if there is *no fftw3f on the target machine* and
if it's an old system which will run its old system until
thrown out, then you could do the /'tough admin'/ solution.

Contact the admin/root of the target machine and let him copy
the files that show up after:

   $ cd /usr
   $ du -a | grep lib64/libfftw3

to the same location (/usr/lib64) on the target machine. This
will most probably work fine (I did so in many cases).

Another variant: Put these files into your user directory
on the target machine (/home/andrey/fftw3) and point
LD_LIBRARY_PATH to this directory by issuing (bash):

$ LD_LIBRARY_PATH=/home/andrey/fftw3:$LD_LIBRARY_PATH  mdrun -v

Regards,

M.

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[gmx-users] Fwd: do_dssp

[Preeti Choudhary]

-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Tue, May 14, 2013 at 8:30 PM
Subject: do_dssp
To: Discussion list for GROMACS users gmx-users@gromacs.org


I am facing problem while using do_dssp.I need to store secondary structure
data every 100 ps.For this I am using -dt option.But I didn't get the
concept of it,what is first time here?What exactly does this dt option do ?
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Re: [gmx-users] Fwd: do_dssp

[Justin Lemkul]

On 5/14/13 11:03 AM, Preeti Choudhary wrote:

-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Tue, May 14, 2013 at 8:30 PM
Subject: do_dssp
To: Discussion list for GROMACS users gmx-users@gromacs.org


I am facing problem while using do_dssp.I need to store secondary structure
data every 100 ps.For this I am using -dt option.But I didn't get the
concept of it,what is first time here?What exactly does this dt option do ?



The -dt option allows you to skip frames.  Since do_dssp is very slow, sometimes 
skipping frames is useful.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Fwd: electrostatic potential map

[andrew ritchie]

Tarak,

That's more of a question for the APBS mailing list, but I'll give it my
best shot, but I would highly suggest you check out
http://www.poissonboltzmann.org/apbs first.

APBS is an implicit solvent electrostatics model, and as such you should be
careful with what explicit solvent you include, ie: water that behaves as
bulk water should probably not be explicitly included in the calculation,
while a water molecule that is persistently hydrogen-bonding to a region of
your protein may better be modeled explicitly.  Including waters may change
the molecule surface definitions (based on the atom radii given to the
water molecule atoms), which will change where the high/low dielectric
boundary occurs.

Water's role in the calculation is the same as any other point charge's
role in the calculation--given a charge and radius, the potential obeys the
Poisson-Boltzmann equation.  The Poisson-Boltzmann equation doesn't care
that the atoms are part of water molecules, it just cares about the charge
on the atoms, the size of the atom (because the atom charges are mapped to
grid points in the system based on the size), and the dielectric of the
region the atom is in.

I hope this was a little bit helpful,
-Andrew Ritchie
The University of Texas at Austin
Department of Chemistry and Biochemistry
The Webb Group


On Mon, May 13, 2013 at 7:04 AM, tarak karmakar tarak20...@gmail.comwrote:

 Dear All,

  I am running a simulation of ligand binding in a protein. Ligand is
 mostly negatively charged, so as expected it should bind to the positive
 region of the protein. To check the possible binding zone, I try to
 calculate or rather visualize the electrostatic potential map of a protein
 in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
 Surprisingly, I see two different types of pictures, in presence and in
 absence of water molecules present in the protein pdb file. In presence of
 water molecules, some regions in the protein are showing positive while in
 absence of water molecules these (same) regions are showing negative
 potential. I don't know, exactly, what is the effect of water molecules in
 this calculations.
 Any short of suggestions would be greatly appreciated. ( I apologize
 for posting bit different topic in this mailing list)
 Thanks and regards,
 Tarak
 --
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[gmx-users] Fwd: Static compilation of gromacs

[Андрей Гончар]

Hi. I'm trying to static compile gromacs from source, everything goes well,
but when I
move it to another machine and try to launch mdrun I got a message:

mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

I run ./configure with the following options:

./configure --prefix=$PREF --enable-all-static --with-x=no --enable-mpi
--without-xml --disable-shared --with-fft=fftw3

The goal is to compile gromacs on one computer and to use it on another. I
haven't root privileges on another machine so I decided to make a
statically linked instance of gromacs, copy it to another computer and use
it from my home directory.

-- 
Andrew Gonchar
Андрей Гончар
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Re: [gmx-users] Fwd: Static compilation of gromacs

[Alexey Shvetsov]

В письме от 15 мая 2013 00:11:49 пользователь Андрей Гончар написал:
 Hi. I'm trying to static compile gromacs from source, everything goes well,
 but when I
 move it to another machine and try to launch mdrun I got a message:
 
 mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open
 shared object file: No such file or directory
 
 I run ./configure with the following options:
 
 ./configure --prefix=$PREF --enable-all-static --with-x=no --enable-mpi
 --without-xml --disable-shared --with-fft=fftw3
 
 The goal is to compile gromacs on one computer and to use it on another. I
 haven't root privileges on another machine so I decided to make a
 statically linked instance of gromacs, copy it to another computer and use
 it from my home directory.

You dont need root privileges to install gromacs for example in ${HOME}/usr
also its good idea to build gromacs on target machine
-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexx...@gmail.com
mailto:ale...@gentoo.org
mailto:ale...@omrb.pnpi.spb.ru

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Re: [gmx-users] Fwd: electrostatic potential map

[tarak karmakar]

Thanks
I have little more confusion about the charges assigned to each of the
atoms from pdb2pqr. With and without water the charges of all the protein
atoms are same! But, then why this type of discrepancy is coming from the
potential map?

Thanks for giving the apbs mailing list address. I'll post there, from now
onwards.


On Tue, May 14, 2013 at 11:41 PM, andrew ritchie
drew.w.ritc...@gmail.comwrote:

 Tarak,

 That's more of a question for the APBS mailing list, but I'll give it my
 best shot, but I would highly suggest you check out
 http://www.poissonboltzmann.org/apbs first.

 APBS is an implicit solvent electrostatics model, and as such you should be
 careful with what explicit solvent you include, ie: water that behaves as
 bulk water should probably not be explicitly included in the calculation,
 while a water molecule that is persistently hydrogen-bonding to a region of
 your protein may better be modeled explicitly.  Including waters may change
 the molecule surface definitions (based on the atom radii given to the
 water molecule atoms), which will change where the high/low dielectric
 boundary occurs.

 Water's role in the calculation is the same as any other point charge's
 role in the calculation--given a charge and radius, the potential obeys the
 Poisson-Boltzmann equation.  The Poisson-Boltzmann equation doesn't care
 that the atoms are part of water molecules, it just cares about the charge
 on the atoms, the size of the atom (because the atom charges are mapped to
 grid points in the system based on the size), and the dielectric of the
 region the atom is in.

 I hope this was a little bit helpful,
 -Andrew Ritchie
 The University of Texas at Austin
 Department of Chemistry and Biochemistry
 The Webb Group


 On Mon, May 13, 2013 at 7:04 AM, tarak karmakar tarak20...@gmail.com
 wrote:

  Dear All,
 
   I am running a simulation of ligand binding in a protein. Ligand is
  mostly negatively charged, so as expected it should bind to the positive
  region of the protein. To check the possible binding zone, I try to
  calculate or rather visualize the electrostatic potential map of a
 protein
  in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
  Surprisingly, I see two different types of pictures, in presence and in
  absence of water molecules present in the protein pdb file. In presence
 of
  water molecules, some regions in the protein are showing positive while
 in
  absence of water molecules these (same) regions are showing negative
  potential. I don't know, exactly, what is the effect of water molecules
 in
  this calculations.
  Any short of suggestions would be greatly appreciated. ( I apologize
  for posting bit different topic in this mailing list)
  Thanks and regards,
  Tarak
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
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  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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 --
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Re: [gmx-users] Fwd: Static compilation of gromacs

[Андрей Гончар]

I know, but on target machine there is a gcc compilator version 4.1, and on
gromacs site they told that this version is broken and 4.5 should used
instead. So I try to compile it on machine with 4.5 version of gcc


2013/5/15 Alexey Shvetsov ale...@omrb.pnpi.spb.ru

 В письме от 15 мая 2013 00:11:49 пользователь Андрей Гончар написал:
  Hi. I'm trying to static compile gromacs from source, everything goes
 well,
  but when I
  move it to another machine and try to launch mdrun I got a message:
 
  mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open
  shared object file: No such file or directory
 
  I run ./configure with the following options:
 
  ./configure --prefix=$PREF --enable-all-static --with-x=no --enable-mpi
  --without-xml --disable-shared --with-fft=fftw3
 
  The goal is to compile gromacs on one computer and to use it on another.
 I
  haven't root privileges on another machine so I decided to make a
  statically linked instance of gromacs, copy it to another computer and
 use
  it from my home directory.

 You dont need root privileges to install gromacs for example in ${HOME}/usr
 also its good idea to build gromacs on target machine
 --
 Best Regards,
 Alexey 'Alexxy' Shvetsov
 Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
 Gatchina, Russia
 Department of Molecular and Radiation Biophysics
 Gentoo Team Ru
 Gentoo Linux Dev
 mailto:alexx...@gmail.com
 mailto:ale...@gentoo.org
 mailto:ale...@omrb.pnpi.spb.ru
 --
 gmx-users mailing listgmx-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!
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-- 
Andrew Gonchar
Андрей Гончар
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[gmx-users] Fwd: electrostatic potential map

[tarak karmakar]

Dear All,

 I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather visualize the electrostatic potential map of a protein
in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
Surprisingly, I see two different types of pictures, in presence and in
absence of water molecules present in the protein pdb file. In presence of
water molecules, some regions in the protein are showing positive while in
absence of water molecules these (same) regions are showing negative
potential. I don't know, exactly, what is the effect of water molecules in
this calculations.
Any short of suggestions would be greatly appreciated. ( I apologize
for posting bit different topic in this mailing list)
Thanks and regards,
Tarak
-- 
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[gmx-users] Fwd: Rycaert-Bellemans function

[Marcelo Vanean]

Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?
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Re: [gmx-users] Fwd: Rycaert-Bellemans function

[Justin Lemkul]

On 5/13/13 6:24 PM, Marcelo Vanean wrote:

Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?



That depends on which force field you are using.  See manual section 4.2.12.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Fwd: Rycaert-Bellemans function

[Dallas Warren]

That really depends on where the function that you are using comes from and 
what forcefield you are using (because each forcefield can treat them 
differently).  If it is the one for alkane chains mentioned in the manual to be 
used with the GROMOS FFs, then as it states in the manual you have to remove 
pairs.  If it comes from the OPLS FFs, then you need to leave the pairs in.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Marcelo Vanean
 Sent: Tuesday, 14 May 2013 8:24 AM
 To: gmx-users@gromacs.org
 Subject: [gmx-users] Fwd: Rycaert-Bellemans function
 
 Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
 used Rycaert-Bellemans function. In this case I should delete the pairs
 from topology?
 --
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[gmx-users] Fwd:

[yakovenko_a]

http://brotherauto.sakura.ne.jp/xcwylh.php

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Re: [gmx-users] Fwd: Selecting the temperature distribution

[Mark Abraham]

Likewise, I agreed with what Massimo said.

As an example, I recently did a fairly large set of REMD simulations of a
320-atom disordered peptide with rather more water and many fewer replicas
than you propose. I did so because I expected low barriers and large
maximum diameter (the latter from an implicit-solvent REMD). Even after the
fact, I cannot demonstrate that my decisions were correct (and probably
could not even if I could have produced clearly converged ensembles).

Mark
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

This hints at an interesting protocol/attempt, at least for a sort of
newbie like me. Can you elaborate? Did they exchange?
On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote:

 Likewise, I agreed with what Massimo said.

 As an example, I recently did a fairly large set of REMD simulations of a
 320-atom disordered peptide with rather more water and many fewer replicas
 than you propose. I did so because I expected low barriers and large
 maximum diameter (the latter from an implicit-solvent REMD). Even after the
 fact, I cannot demonstrate that my decisions were correct (and probably
 could not even if I could have produced clearly converged ensembles).

 Mark
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[Mark Abraham]

Yes,  I got exchanges. By construction! :-)

Email me off-list if you would like a methods description (for what it is
worth).

Mark


On Thu, Apr 25, 2013 at 1:11 PM, massimo sandal deviceran...@gmail.comwrote:

 This hints at an interesting protocol/attempt, at least for a sort of
 newbie like me. Can you elaborate? Did they exchange?
 On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote:

  Likewise, I agreed with what Massimo said.
 
  As an example, I recently did a fairly large set of REMD simulations of a
  320-atom disordered peptide with rather more water and many fewer
 replicas
  than you propose. I did so because I expected low barriers and large
  maximum diameter (the latter from an implicit-solvent REMD). Even after
 the
  fact, I cannot demonstrate that my decisions were correct (and probably
  could not even if I could have produced clearly converged ensembles).
 
  Mark
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Re: [gmx-users] Fwd: amber03 force field

[Mark Abraham]

X-C-CN-X is not present in amber03 in the GROMACS distribution. You seem to
be using some modified version. Please ask the person who modified it :-)

Mark


On Wed, Apr 24, 2013 at 4:26 PM, Elisa Frezza elisa.fre...@gmail.comwrote:

 Dear All,

 I am starting to use amber03 force field, but I have found something very
 strange for proper angle dihedral.

 On the basis of definition of proper dihedral function in AMBER and GROMACS
 manual I aspect that the following conversion from amber to gromacs:

 k_n(GROMACS)=4.18/2 V_n (AMBER)

 where n= multiplicity.

 If I compare ffbonded.itp file in ffamber03 folder and the parameter
 reported in amber I find something very strange and I do not understand
 what it is right:

constant   angle
multiplicity
 AMBER:   X   CCNX8.00 180 2
 GROMACS   X   CCNX  16.736180 2
# kn= 4.18/2 V_n

constant   angle
multiplicity
 AMBER:   X   CNAX5.648 180
 2
 GROMACS   X   CNAX5.648 180 2
  # kn= 4.18/4 V_n

 the ratios between kn and Vn are different.
 Have someone some suggestions or explanation?

 Thanks in advance

 Elisa

 --
 Elisa Frezza
 Ph.D. Student in Materials Science and Engineering
 Dipartimento di Scienze Chimiche
 Università di Padova
 via Marzolo, 1
 35131 Padova - Italy
 Phone: +39 049 827 5149
 Skype: elisa.frezza
 Emai: elisa.fre...@gmail.com
  elisa.fre...@studenti.unipd.it





 --
 Elisa Frezza
 Ph.D. Student in Materials Science and Engineering
 Dipartimento di Scienze Chimiche
 Università di Padova
 via Marzolo, 1
 35131 Padova - Italy
 Phone: +39 049 827 5149
 Skype: elisa.frezza
 Emai: elisa.fre...@gmail.com
  elisa.fre...@studenti.unipd.it
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[Justin Lemkul]

On 4/23/13 9:43 PM, bharat gupta wrote:

Dear Justin/Mark,

I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is from 300 to
500. I want to select appropriate temp. for 56 replicas (as I have 56
processors available). I used the t-remd calculator for temp. generation.
It provided some 200 temp. values. Here are my questions :
1. Is it possible to select equally spaced temp. values from those values ??
2. I checked that reducing the no. of water mol. decreases the temp.
values. What if I reduce the no. of water mol., will if affect the
simulation ??



I haven't said anything because I agree with what Massimo has already told you. 
 If that is comforting in some way to know, then so be it, but I think it is 
rather rude to suggest that you would rather someone else answer your question, 
even after being given thorough and correct insight.  This is a community forum 
with many experts who have valuable insight to share.


-Justin




On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal deviceran...@gmail.comwrote:


In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).

Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent results, reviewers might not be
happy. There is a chance that the results coming out of your simulation
might be nonsense. Discuss this choice with your supervisor and/or with
expert colleagues who know about limitations of implicit solvent. You need
to be able to justify your choice scientifically -for example testing it
with a known,similar system and observing that implicit solvent reproduces
the behaviour of that system in explicit solvent well.

About reducing the box size, by all means try it, but always make sure it
is large enough to avoid that the periodic copies of your molecule see each
other. See

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.


2013/4/23 bharat gupta bharat.85.m...@gmail.com


Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced ,

the

no. of temp. values are also reduced. If I reduce the no. of water
molecules or reduce the size of box , will it help. As of now I am using
octahedron box.


On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.com

wrote:



It depends on what you want to do. Possible it is certainly possible,

but

you can't be guaranteed to observe the conformational changes you

desire

to

observe. Again, it does not depend only on the REMD, but also on the

length

of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also

depends

on your system itself -and this you cannot know without trying.

If you want to improve sampling beyond what standard REMD can do, to
exploit your computational resources at the best, you can look into

other

approaches like solute tempering (
http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to

study

*well* this kind of things, talk with experts in these techniques,  and
remember that there is no guarantee any of them will bring the result

you

want. Good luck! :)




2013/4/23 bharat gupta bharat.85.m...@gmail.com


So, my final question is whether is possible to do REMD for my

system,

using the computational resource that I have.


On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal 

deviceran...@gmail.com

wrote:



Who knows? It depends on the size of your peptide, on the energy

landscape,

on how long is the run you plan to do. I would bet on no,

however.



2013/4/23 bharat gupta bharat.85.m...@gmail.com


But if I choose a smaller temperature range , would it be

possible

to

observe any folding event ??


On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 

deviceran...@gmail.com

wrote:



Thanks, now it's clearer.


Now, how can I temp. from these, so that the replicas can

exchange

...


You can't, I would say. The system you have requires so many

replicas

to

exchange properly from the two temperature extremes you set up.

As

you

have

seen, if you pick up temperatures in that range randomly, they

can't

exchange anymore. They are too far away.

I would choose a smaller temperature range. There is little

else

you

can

do, I think.


2013/4/23 bharat gupta bharat.85.m...@gmail.com


Sorry for that, I explain it again. Actually, I used the this

link

to

generate a temp. distribution. But I can do REMD for 56

replicas

only,

as I

have 56 

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

2013/4/24 Justin Lemkul jalem...@vt.edu



 I haven't said anything because I agree with what Massimo has already told
 you.  If that is comforting in some way to know, then so be it, but I think
 it is rather rude to suggest that you would rather someone else answer your
 question, even after being given thorough and correct insight.  This is a
 community forum with many experts who have valuable insight to share.


Well, he couldn't know that my insight was right (honestly, I was expecting
to be corrected!). I think he did right by trying to be double-sure, I
don't feel offended by it :)
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

I think it should be me who should be sorry. I should have asked the
question again in the forum without referring to some particular
individual.


On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.comwrote:

 2013/4/24 Justin Lemkul jalem...@vt.edu

 
 
  I haven't said anything because I agree with what Massimo has already
 told
  you.  If that is comforting in some way to know, then so be it, but I
 think
  it is rather rude to suggest that you would rather someone else answer
 your
  question, even after being given thorough and correct insight.  This is a
  community forum with many experts who have valuable insight to share.
 

 Well, he couldn't know that my insight was right (honestly, I was expecting
 to be corrected!). I think he did right by trying to be double-sure, I
 don't feel offended by it :)
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
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[gmx-users] Fwd: amber03 force field

[Elisa Frezza]

Dear All,

I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.

On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:

k_n(GROMACS)=4.18/k V_n (AMBER)

where n= multiplicity.

If I compare ffbonded.itp file in ffamber03 folder and the parameter
reported in amber I find something very strange and I do not understand
what it is right:

   constant   angle
 multiplicity
AMBER:   X   CCNX8.00 180 2
GROMACS

-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it





-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it
--
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[gmx-users] Fwd: amber03 force field

[Elisa Frezza]

Dear All,

I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.

On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:

k_n(GROMACS)=4.18/2 V_n (AMBER)

where n= multiplicity.

If I compare ffbonded.itp file in ffamber03 folder and the parameter
reported in amber I find something very strange and I do not understand
what it is right:

   constant   angle
   multiplicity
AMBER:   X   CCNX8.00 180 2
GROMACS   X   CCNX  16.736180 2
   # kn= 4.18/2 V_n

   constant   angle
   multiplicity
AMBER:   X   CNAX5.648 180 2
GROMACS   X   CNAX5.648 180 2
 # kn= 4.18/4 V_n

the ratios between kn and Vn are different.
Have someone some suggestions or explanation?

Thanks in advance

Elisa

-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it





-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Don't be sorry. It's okay. It's just cultural differences.


2013/4/24 bharat gupta bharat.85.m...@gmail.com

 I think it should be me who should be sorry. I should have asked the
 question again in the forum without referring to some particular
 individual.


 On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.com
 wrote:

  2013/4/24 Justin Lemkul jalem...@vt.edu
 
  
  
   I haven't said anything because I agree with what Massimo has already
  told
   you.  If that is comforting in some way to know, then so be it, but I
  think
   it is rather rude to suggest that you would rather someone else answer
  your
   question, even after being given thorough and correct insight.  This
 is a
   community forum with many experts who have valuable insight to share.
  
 
  Well, he couldn't know that my insight was right (honestly, I was
 expecting
  to be corrected!). I think he did right by trying to be double-sure, I
  don't feel offended by it :)
  --
  gmx-users mailing listgmx-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!
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  www interface or send it to gmx-users-requ...@gromacs.org.
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 --
 Bharat
 Ph.D. Candidate
 Biomolecular Engineering Laboratory
 Pusan National University
 South Korea
 Mobile no. - 010-5818-3680
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Dear gmx users,

I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can use
the formula  Ti=T0*ek*i, but what is the value for i and K here ??


BHARAT
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Look here: http://folding.bmc.uu.se/remd/



2013/4/23 bharat gupta bharat.85.m...@gmail.com

 Dear gmx users,

 I am planning to run REMD for a peptide (406 atoms )+ solvent system
 (27639). The temperature range I selected is from 300 to 500. I want to
 select appropriate temp. for 56 replicas. I randomly chose some temp
 distribution and the exchange probabilities was 0.0. I know that we can use
 the formula  Ti=T0*ek*i, but what is the value for i and K here ??

 
 BHARAT
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that


On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.comwrote:

 Look here: http://folding.bmc.uu.se/remd/



 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  Dear gmx users,
 
  I am planning to run REMD for a peptide (406 atoms )+ solvent system
  (27639). The temperature range I selected is from 300 to 500. I want to
  select appropriate temp. for 56 replicas. I randomly chose some temp
  distribution and the exchange probabilities was 0.0. I know that we can
 use
  the formula  Ti=T0*ek*i, but what is the value for i and K here ??
 
  
  BHARAT
  --
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

I don't understand your question. If you got the temperature distribution,
what else do you need?


2013/4/23 bharat gupta bharat.85.m...@gmail.com

 I have got the temperature distribution from the same link, but how to
 select evenly spaced temperatures for 56 replicas, I need to know that


 On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.com
 wrote:

  Look here: http://folding.bmc.uu.se/remd/
 
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   Dear gmx users,
  
   I am planning to run REMD for a peptide (406 atoms )+ solvent system
   (27639). The temperature range I selected is from 300 to 500. I want to
   select appropriate temp. for 56 replicas. I randomly chose some temp
   distribution and the exchange probabilities was 0.0. I know that we can
  use
   the formula  Ti=T0*ek*i, but what is the value for i and K here ??
  
   
   BHARAT
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas only, as I
have 56 processors available. The t-remd calculator provides 220
temperature values :

300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
595.24, 597.04, 598.85, 600.66


Now, how can I temp. from these, so that the replicas can exchange ...


On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.comwrote:

 I don't understand your question. If you got the temperature distribution,
 what else do you need?


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  I have got the temperature distribution from the same link, but how to
  select evenly spaced temperatures for 56 replicas, I need to know that
 
 
  On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.com
  wrote:
 
   Look here: http://folding.bmc.uu.se/remd/
  
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
Dear gmx users,
   
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want
 to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we
 can
   use
the formula  Ti=T0*ek*i, but what is the value for i and K here ??
   

BHARAT
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-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Thanks, now it's clearer.

 Now, how can I temp. from these, so that the replicas can exchange ...

You can't, I would say. The system you have requires so many replicas to
exchange properly from the two temperature extremes you set up. As you have
seen, if you pick up temperatures in that range randomly, they can't
exchange anymore. They are too far away.

I would choose a smaller temperature range. There is little else you can
do, I think.


2013/4/23 bharat gupta bharat.85.m...@gmail.com

 Sorry for that, I explain it again. Actually, I used the this link to
 generate a temp. distribution. But I can do REMD for 56 replicas only, as I
 have 56 processors available. The t-remd calculator provides 220
 temperature values :

 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
 595.24, 597.04, 598.85, 600.66


 Now, how can I temp. from these, so that the replicas can exchange ...


 On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.com
 wrote:

  I don't understand your question. If you got the temperature
 distribution,
  what else do you need?
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   I have got the temperature distribution from the same link, but how to
   select evenly spaced temperatures for 56 replicas, I need to know that
  
  
   On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
Look here: http://folding.bmc.uu.se/remd/
   
   
   
2013/4/23 bharat gupta bharat.85.m...@gmail.com
   
 Dear gmx users,

 I am planning to run REMD for a peptide (406 atoms )+ solvent
 system
 (27639). The temperature range I selected is from 300 to 500. I
 want
  to
 select appropriate temp. for 56 replicas. I randomly chose some
 temp
 distribution and the exchange probabilities was 0.0. I know that we
  can
use
 the formula  Ti=T0*ek*i, but what is the value for i and K here ??

 
 BHARAT
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

But if I choose a smaller temperature range , would it be possible to
observe any folding event ??


On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.comwrote:

 Thanks, now it's clearer.

  Now, how can I temp. from these, so that the replicas can exchange ...

 You can't, I would say. The system you have requires so many replicas to
 exchange properly from the two temperature extremes you set up. As you have
 seen, if you pick up temperatures in that range randomly, they can't
 exchange anymore. They are too far away.

 I would choose a smaller temperature range. There is little else you can
 do, I think.


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  Sorry for that, I explain it again. Actually, I used the this link to
  generate a temp. distribution. But I can do REMD for 56 replicas only,
 as I
  have 56 processors available. The t-remd calculator provides 220
  temperature values :
 
  300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
  309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
  318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
  328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
  338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
  348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
  358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
  369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
  380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
  391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
  402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
  414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
  426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
  438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
  451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
  464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
  477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
  490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
  504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
  518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
  533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
  548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
  563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
  579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
  595.24, 597.04, 598.85, 600.66
 
 
  Now, how can I temp. from these, so that the replicas can exchange ...
 
 
  On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.com
  wrote:
 
   I don't understand your question. If you got the temperature
  distribution,
   what else do you need?
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
I have got the temperature distribution from the same link, but how
 to
select evenly spaced temperatures for 56 replicas, I need to know
 that
   
   
On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal 
  deviceran...@gmail.com
wrote:
   
 Look here: http://folding.bmc.uu.se/remd/



 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  Dear gmx users,
 
  I am planning to run REMD for a peptide (406 atoms )+ solvent
  system
  (27639). The temperature range I selected is from 300 to 500. I
  want
   to
  select appropriate temp. for 56 replicas. I randomly chose some
  temp
  distribution and the exchange probabilities was 0.0. I know that
 we
   can
 use
  the formula  Ti=T0*ek*i, but what is the value for i and K here
 ??
 
  
  BHARAT
  --
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before
  posting!
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Who knows? It depends on the size of your peptide, on the energy landscape,
on how long is the run you plan to do. I would bet on no, however.


2013/4/23 bharat gupta bharat.85.m...@gmail.com

 But if I choose a smaller temperature range , would it be possible to
 observe any folding event ??


 On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com
 wrote:

  Thanks, now it's clearer.
 
   Now, how can I temp. from these, so that the replicas can exchange ...
 
  You can't, I would say. The system you have requires so many replicas to
  exchange properly from the two temperature extremes you set up. As you
 have
  seen, if you pick up temperatures in that range randomly, they can't
  exchange anymore. They are too far away.
 
  I would choose a smaller temperature range. There is little else you can
  do, I think.
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   Sorry for that, I explain it again. Actually, I used the this link to
   generate a temp. distribution. But I can do REMD for 56 replicas only,
  as I
   have 56 processors available. The t-remd calculator provides 220
   temperature values :
  
   300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
   309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
   318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
   328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
   338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
   348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
   358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
   369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
   380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
   391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
   402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
   414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
   426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
   438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
   451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
   464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
   477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
   490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
   504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
   518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
   533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
   548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
   563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
   579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
   595.24, 597.04, 598.85, 600.66
  
  
   Now, how can I temp. from these, so that the replicas can exchange ...
  
  
   On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
I don't understand your question. If you got the temperature
   distribution,
what else do you need?
   
   
2013/4/23 bharat gupta bharat.85.m...@gmail.com
   
 I have got the temperature distribution from the same link, but how
  to
 select evenly spaced temperatures for 56 replicas, I need to know
  that


 On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal 
   deviceran...@gmail.com
 wrote:

  Look here: http://folding.bmc.uu.se/remd/
 
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   Dear gmx users,
  
   I am planning to run REMD for a peptide (406 atoms )+ solvent
   system
   (27639). The temperature range I selected is from 300 to 500. I
   want
to
   select appropriate temp. for 56 replicas. I randomly chose some
   temp
   distribution and the exchange probabilities was 0.0. I know
 that
  we
can
  use
   the formula  Ti=T0*ek*i, but what is the value for i and K here
  ??
  
   
   BHARAT
   --
   gmx-users mailing listgmx-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
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

So, my final question is whether is possible to do REMD for my system,
using the computational resource that I have.


On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.comwrote:

 Who knows? It depends on the size of your peptide, on the energy landscape,
 on how long is the run you plan to do. I would bet on no, however.


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  But if I choose a smaller temperature range , would it be possible to
  observe any folding event ??
 
 
  On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com
  wrote:
 
   Thanks, now it's clearer.
  
Now, how can I temp. from these, so that the replicas can exchange
 ...
  
   You can't, I would say. The system you have requires so many replicas
 to
   exchange properly from the two temperature extremes you set up. As you
  have
   seen, if you pick up temperatures in that range randomly, they can't
   exchange anymore. They are too far away.
  
   I would choose a smaller temperature range. There is little else you
 can
   do, I think.
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas
 only,
   as I
have 56 processors available. The t-remd calculator provides 220
temperature values :
   
300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
 308.17,
309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
 317.56,
318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
 327.18,
328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
 337.04,
338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
 347.13,
348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
 357.47,
358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
 368.05,
369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
 378.90,
380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
 390.00,
391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
 401.38,
402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
 413.05,
414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
 425.03,
426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
 437.26,
438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
 449.79,
451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
 462.63,
464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
 475.80,
477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
 489.27,
490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
 503.07,
504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
 517.24,
518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
 531.73,
533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
 546.56,
548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
 561.76,
563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
 577.47,
579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
 593.44,
595.24, 597.04, 598.85, 600.66
   
   
Now, how can I temp. from these, so that the replicas can exchange
 ...
   
   
On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal 
  deviceran...@gmail.com
wrote:
   
 I don't understand your question. If you got the temperature
distribution,
 what else do you need?


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  I have got the temperature distribution from the same link, but
 how
   to
  select evenly spaced temperatures for 56 replicas, I need to know
   that
 
 
  On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal 
deviceran...@gmail.com
  wrote:
 
   Look here: http://folding.bmc.uu.se/remd/
  
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
Dear gmx users,
   
I am planning to run REMD for a peptide (406 atoms )+ solvent
system
(27639). The temperature range I selected is from 300 to
 500. I
want
 to
select appropriate temp. for 56 replicas. I randomly chose
 some
temp
distribution and the exchange probabilities was 0.0. I know
  that
   we
 can
   use
the formula  Ti=T0*ek*i, but what is the value for i and K
 here
   ??
   

BHARAT
--
gmx-users mailing listgmx-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
  

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

It depends on what you want to do. Possible it is certainly possible, but
you can't be guaranteed to observe the conformational changes you desire to
observe. Again, it does not depend only on the REMD, but also on the length
of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
on your system itself -and this you cannot know without trying.

If you want to improve sampling beyond what standard REMD can do, to
exploit your computational resources at the best, you can look into other
approaches like solute tempering (
http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study
*well* this kind of things, talk with experts in these techniques,  and
remember that there is no guarantee any of them will bring the result you
want. Good luck! :)




2013/4/23 bharat gupta bharat.85.m...@gmail.com

 So, my final question is whether is possible to do REMD for my system,
 using the computational resource that I have.


 On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.com
 wrote:

  Who knows? It depends on the size of your peptide, on the energy
 landscape,
  on how long is the run you plan to do. I would bet on no, however.
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   But if I choose a smaller temperature range , would it be possible to
   observe any folding event ??
  
  
   On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
Thanks, now it's clearer.
   
 Now, how can I temp. from these, so that the replicas can exchange
  ...
   
You can't, I would say. The system you have requires so many replicas
  to
exchange properly from the two temperature extremes you set up. As
 you
   have
seen, if you pick up temperatures in that range randomly, they can't
exchange anymore. They are too far away.
   
I would choose a smaller temperature range. There is little else you
  can
do, I think.
   
   
2013/4/23 bharat gupta bharat.85.m...@gmail.com
   
 Sorry for that, I explain it again. Actually, I used the this link
 to
 generate a temp. distribution. But I can do REMD for 56 replicas
  only,
as I
 have 56 processors available. The t-remd calculator provides 220
 temperature values :

 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
  308.17,
 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
  317.56,
 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
  327.18,
 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
  337.04,
 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
  347.13,
 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
  357.47,
 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
  368.05,
 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
  378.90,
 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
  390.00,
 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
  401.38,
 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
  413.05,
 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
  425.03,
 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
  437.26,
 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
  449.79,
 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
  462.63,
 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
  475.80,
 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
  489.27,
 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
  503.07,
 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
  517.24,
 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
  531.73,
 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
  546.56,
 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
  561.76,
 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
  577.47,
 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
  593.44,
 595.24, 597.04, 598.85, 600.66


 Now, how can I temp. from these, so that the replicas can exchange
  ...


 On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal 
   deviceran...@gmail.com
 wrote:

  I don't understand your question. If you got the temperature
 distribution,
  what else do you need?
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   I have got the temperature distribution from the same link, but
  how
to
   select evenly spaced temperatures for 56 replicas, I need to
 know
that
  
  
   On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
Look here: http://folding.bmc.uu.se/remd/
   

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

In general, look in the literature what other people have done on similar
systems, and try to go from there.


2013/4/23 massimo sandal deviceran...@gmail.com

 It depends on what you want to do. Possible it is certainly possible, but
 you can't be guaranteed to observe the conformational changes you desire to
 observe. Again, it does not depend only on the REMD, but also on the length
 of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
 on your system itself -and this you cannot know without trying.

 If you want to improve sampling beyond what standard REMD can do, to
 exploit your computational resources at the best, you can look into other
 approaches like solute tempering (
 http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
 http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
 study *well* this kind of things, talk with experts in these techniques,
 and remember that there is no guarantee any of them will bring the result
 you want. Good luck! :)




 2013/4/23 bharat gupta bharat.85.m...@gmail.com

 So, my final question is whether is possible to do REMD for my system,
 using the computational resource that I have.


 On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.com
 wrote:

  Who knows? It depends on the size of your peptide, on the energy
 landscape,
  on how long is the run you plan to do. I would bet on no, however.
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   But if I choose a smaller temperature range , would it be possible to
   observe any folding event ??
  
  
   On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
Thanks, now it's clearer.
   
 Now, how can I temp. from these, so that the replicas can exchange
  ...
   
You can't, I would say. The system you have requires so many
 replicas
  to
exchange properly from the two temperature extremes you set up. As
 you
   have
seen, if you pick up temperatures in that range randomly, they can't
exchange anymore. They are too far away.
   
I would choose a smaller temperature range. There is little else you
  can
do, I think.
   
   
2013/4/23 bharat gupta bharat.85.m...@gmail.com
   
 Sorry for that, I explain it again. Actually, I used the this
 link to
 generate a temp. distribution. But I can do REMD for 56 replicas
  only,
as I
 have 56 processors available. The t-remd calculator provides 220
 temperature values :

 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
  308.17,
 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
  317.56,
 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
  327.18,
 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
  337.04,
 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
  347.13,
 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
  357.47,
 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
  368.05,
 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
  378.90,
 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
  390.00,
 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
  401.38,
 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
  413.05,
 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
  425.03,
 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
  437.26,
 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
  449.79,
 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
  462.63,
 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
  475.80,
 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
  489.27,
 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
  503.07,
 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
  517.24,
 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
  531.73,
 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
  546.56,
 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
  561.76,
 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
  577.47,
 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
  593.44,
 595.24, 597.04, 598.85, 600.66


 Now, how can I temp. from these, so that the replicas can exchange
  ...


 On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal 
   deviceran...@gmail.com
 wrote:

  I don't understand your question. If you got the temperature
 distribution,
  what else do you need?
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   I have got the temperature distribution from the same link,
 but
  how
to
   select evenly spaced temperatures for 56 replicas, I need to
 know
that
 

Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced , the
no. of temp. values are also reduced. If I reduce the no. of water
molecules or reduce the size of box , will it help. As of now I am using
octahedron box.


On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.comwrote:

 It depends on what you want to do. Possible it is certainly possible, but
 you can't be guaranteed to observe the conformational changes you desire to
 observe. Again, it does not depend only on the REMD, but also on the length
 of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
 on your system itself -and this you cannot know without trying.

 If you want to improve sampling beyond what standard REMD can do, to
 exploit your computational resources at the best, you can look into other
 approaches like solute tempering (
 http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
 http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study
 *well* this kind of things, talk with experts in these techniques,  and
 remember that there is no guarantee any of them will bring the result you
 want. Good luck! :)




 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  So, my final question is whether is possible to do REMD for my system,
  using the computational resource that I have.
 
 
  On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.com
  wrote:
 
   Who knows? It depends on the size of your peptide, on the energy
  landscape,
   on how long is the run you plan to do. I would bet on no, however.
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
But if I choose a smaller temperature range , would it be possible to
observe any folding event ??
   
   
On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 
  deviceran...@gmail.com
wrote:
   
 Thanks, now it's clearer.

  Now, how can I temp. from these, so that the replicas can
 exchange
   ...

 You can't, I would say. The system you have requires so many
 replicas
   to
 exchange properly from the two temperature extremes you set up. As
  you
have
 seen, if you pick up temperatures in that range randomly, they
 can't
 exchange anymore. They are too far away.

 I would choose a smaller temperature range. There is little else
 you
   can
 do, I think.


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  Sorry for that, I explain it again. Actually, I used the this
 link
  to
  generate a temp. distribution. But I can do REMD for 56 replicas
   only,
 as I
  have 56 processors available. The t-remd calculator provides 220
  temperature values :
 
  300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
   308.17,
  309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
   317.56,
  318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
   327.18,
  328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
   337.04,
  338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
   347.13,
  348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
   357.47,
  358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
   368.05,
  369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
   378.90,
  380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
   390.00,
  391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
   401.38,
  402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
   413.05,
  414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
   425.03,
  426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
   437.26,
  438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
   449.79,
  451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
   462.63,
  464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
   475.80,
  477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
   489.27,
  490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
   503.07,
  504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
   517.24,
  518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
   531.73,
  533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
   546.56,
  548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
   561.76,
  563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
   577.47,
  579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
   593.44,
  595.24, 597.04, 598.85, 600.66
 
 
  Now, how can I temp. from these, so that the replicas can
 exchange
   ...
 
 
  On Tue, Apr 23, 2013 at 9:04 PM, 

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).

Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent results, reviewers might not be
happy. There is a chance that the results coming out of your simulation
might be nonsense. Discuss this choice with your supervisor and/or with
expert colleagues who know about limitations of implicit solvent. You need
to be able to justify your choice scientifically -for example testing it
with a known,similar system and observing that implicit solvent reproduces
the behaviour of that system in explicit solvent well.

About reducing the box size, by all means try it, but always make sure it
is large enough to avoid that the periodic copies of your molecule see each
other. See
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.


2013/4/23 bharat gupta bharat.85.m...@gmail.com

 Thanks a lot for your prompt responses. By using implicit solvent , I am
 getting on 9 temperature values. I think this should work , I will try it
 out. Also, i checked that when the no. of water molecules are reduced , the
 no. of temp. values are also reduced. If I reduce the no. of water
 molecules or reduce the size of box , will it help. As of now I am using
 octahedron box.


 On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.com
 wrote:

  It depends on what you want to do. Possible it is certainly possible, but
  you can't be guaranteed to observe the conformational changes you desire
 to
  observe. Again, it does not depend only on the REMD, but also on the
 length
  of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
 depends
  on your system itself -and this you cannot know without trying.
 
  If you want to improve sampling beyond what standard REMD can do, to
  exploit your computational resources at the best, you can look into other
  approaches like solute tempering (
  http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
  http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
 study
  *well* this kind of things, talk with experts in these techniques,  and
  remember that there is no guarantee any of them will bring the result you
  want. Good luck! :)
 
 
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   So, my final question is whether is possible to do REMD for my system,
   using the computational resource that I have.
  
  
   On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal 
 deviceran...@gmail.com
   wrote:
  
Who knows? It depends on the size of your peptide, on the energy
   landscape,
on how long is the run you plan to do. I would bet on no, however.
   
   
2013/4/23 bharat gupta bharat.85.m...@gmail.com
   
 But if I choose a smaller temperature range , would it be possible
 to
 observe any folding event ??


 On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 
   deviceran...@gmail.com
 wrote:

  Thanks, now it's clearer.
 
   Now, how can I temp. from these, so that the replicas can
  exchange
...
 
  You can't, I would say. The system you have requires so many
  replicas
to
  exchange properly from the two temperature extremes you set up.
 As
   you
 have
  seen, if you pick up temperatures in that range randomly, they
  can't
  exchange anymore. They are too far away.
 
  I would choose a smaller temperature range. There is little else
  you
can
  do, I think.
 
 
  2013/4/23 bharat gupta bharat.85.m...@gmail.com
 
   Sorry for that, I explain it again. Actually, I used the this
  link
   to
   generate a temp. distribution. But I can do REMD for 56
 replicas
only,
  as I
   have 56 processors available. The t-remd calculator provides
 220
   temperature values :
  
   300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
308.17,
   309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
317.56,
   318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
327.18,
   328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
337.04,
   338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
347.13,
   348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
357.47,
   358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
368.05,
   369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
378.90,
   380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
390.00,
   391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
401.38,
   402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
413.05,
   414.40, 415.71, 417.03, 418.36, 

Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Dear Justin/Mark,

I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is from 300 to
500. I want to select appropriate temp. for 56 replicas (as I have 56
processors available). I used the t-remd calculator for temp. generation.
It provided some 200 temp. values. Here are my questions :
1. Is it possible to select equally spaced temp. values from those values ??
2. I checked that reducing the no. of water mol. decreases the temp.
values. What if I reduce the no. of water mol., will if affect the
simulation ??



On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal deviceran...@gmail.comwrote:

 In general, the smaller is your system, the less temperatures you will need
 (and you'll have better performance).

 Notice however that implicit solvent, while surely a possibility worth
 considering, is not usually considered to be very good -take care that if
 you write a paper from implicit solvent results, reviewers might not be
 happy. There is a chance that the results coming out of your simulation
 might be nonsense. Discuss this choice with your supervisor and/or with
 expert colleagues who know about limitations of implicit solvent. You need
 to be able to justify your choice scientifically -for example testing it
 with a known,similar system and observing that implicit solvent reproduces
 the behaviour of that system in explicit solvent well.

 About reducing the box size, by all means try it, but always make sure it
 is large enough to avoid that the periodic copies of your molecule see each
 other. See

 http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
 be sure to understand it.


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  Thanks a lot for your prompt responses. By using implicit solvent , I am
  getting on 9 temperature values. I think this should work , I will try it
  out. Also, i checked that when the no. of water molecules are reduced ,
 the
  no. of temp. values are also reduced. If I reduce the no. of water
  molecules or reduce the size of box , will it help. As of now I am using
  octahedron box.
 
 
  On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.com
  wrote:
 
   It depends on what you want to do. Possible it is certainly possible,
 but
   you can't be guaranteed to observe the conformational changes you
 desire
  to
   observe. Again, it does not depend only on the REMD, but also on the
  length
   of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
  depends
   on your system itself -and this you cannot know without trying.
  
   If you want to improve sampling beyond what standard REMD can do, to
   exploit your computational resources at the best, you can look into
 other
   approaches like solute tempering (
   http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
   http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
  study
   *well* this kind of things, talk with experts in these techniques,  and
   remember that there is no guarantee any of them will bring the result
 you
   want. Good luck! :)
  
  
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
So, my final question is whether is possible to do REMD for my
 system,
using the computational resource that I have.
   
   
On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal 
  deviceran...@gmail.com
wrote:
   
 Who knows? It depends on the size of your peptide, on the energy
landscape,
 on how long is the run you plan to do. I would bet on no,
 however.


 2013/4/23 bharat gupta bharat.85.m...@gmail.com

  But if I choose a smaller temperature range , would it be
 possible
  to
  observe any folding event ??
 
 
  On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal 
deviceran...@gmail.com
  wrote:
 
   Thanks, now it's clearer.
  
Now, how can I temp. from these, so that the replicas can
   exchange
 ...
  
   You can't, I would say. The system you have requires so many
   replicas
 to
   exchange properly from the two temperature extremes you set up.
  As
you
  have
   seen, if you pick up temperatures in that range randomly, they
   can't
   exchange anymore. They are too far away.
  
   I would choose a smaller temperature range. There is little
 else
   you
 can
   do, I think.
  
  
   2013/4/23 bharat gupta bharat.85.m...@gmail.com
  
Sorry for that, I explain it again. Actually, I used the this
   link
to
generate a temp. distribution. But I can do REMD for 56
  replicas
 only,
   as I
have 56 processors available. The t-remd calculator provides
  220
temperature values :
   

[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation

[Parul tew]

Dear GMX users,
 I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I wanted
to modify the parameter files of lipids taken from peter teilman site.
Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6
and c12 to sigma epsilon using formula
Sigma = (c12/c6)^1/6
and
epsilon = c6/(4*sigma^6)
i tried it for the [pairtypes] in lipid.itp file, but the calculations I
made using excel gave me the following:

[ pairtypes ]
;   i   j   funct   sigma   epsilon
LO  LO  1   1.10E-012.96E-01
LO  LOM 1   1.10E-012.96E-0


and so on i.e. the values of sigma and epsilon are interchanged, as
opposed to the values listed by chris neale in archive mail (listed
below)

[ pairtypes ]

;   i   j   funct   sigma   epsilon
LO  LO  1   2.96E-011.10E-01
LO  LOM 1   2.96E-011.10E-01
LO  opls_1161   3.06E-019.47E-02
LO  LNL 1   3.10E-019.88E-02
LO  LC  1   3.33E-017.76E-02
etc...

I am doing something wrong or I can just interchange the values and
use them accordingly.

Thanking you

Parul Tewatia
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Re: [gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation

[Justin Lemkul]

On 4/15/13 6:25 AM, Parul tew wrote:

Dear GMX users,
  I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I wanted
to modify the parameter files of lipids taken from peter teilman site.
Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6
and c12 to sigma epsilon using formula
Sigma = (c12/c6)^1/6
and
epsilon = c6/(4*sigma^6)
i tried it for the [pairtypes] in lipid.itp file, but the calculations I
made using excel gave me the following:

[ pairtypes ]
;   i   j   funct   sigma   epsilon
 LO  LO  1   1.10E-012.96E-01
 LO  LOM 1   1.10E-012.96E-0


and so on i.e. the values of sigma and epsilon are interchanged, as
opposed to the values listed by chris neale in archive mail (listed
below)

[ pairtypes ]

;   i   j   funct   sigma   epsilon
 LO  LO  1   2.96E-011.10E-01
 LO  LOM 1   2.96E-011.10E-01
 LO  opls_1161   3.06E-019.47E-02
 LO  LNL 1   3.10E-019.88E-02
 LO  LC  1   3.33E-017.76E-02
etc...

I am doing something wrong or I can just interchange the values and
use them accordingly.



I think you're doing the calculation wrong, but I can't say exactly how.  If I 
calculate (1.987E-7 / 2.952E-4) ^ (1/6), it comes out to the correct sigma value 
of 0.29603763.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: [Fwd: QM MM modification]

[Mark Abraham]

Hi Natalia,

I am not aware whether the QM/MM implementation in GROMACS works in 4.6,
nor with which Gaussian version was intended to work in the past. Perhaps
Gerrit Groenhof or someone on gmx-users can update us here?

I'm not sure what diff file you are seeking, either. Can you elaborate
please?

Mark

-- Forwarded message --
From: ku...@nh.cas.cz
Date: Fri, Apr 12, 2013 at 1:53 PM
Subject: [Fwd: QM MM modification]
To: mark.abra...@scilifelab.se


Good afternoon! My name is Natallia Kulik and I am working in Czech
Academy of Sciences on the project of simulation oh substrate-enzyme
interaction of hexosaminidases.
I want to use Gromacs 4.6 with QM implementation (Gaussian 09) for my
calculation. However unfortunately we can't correctly change gaussian
file. Could you, please, send us diff-file from the original version of
gaussian (for gaussian 09 or 03)?

Thank you very much, Natallia
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Re: [gmx-users] Fwd: rmsd

[Preeti Choudhary]

Thankyou


On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary 
 preetichoudhary18111...@gmail.com wrote:

  -- Forwarded message --
  From: Preeti Choudhary preetichoudhary18111...@gmail.com
  Date: Wed, Apr 10, 2013 at 7:46 PM
  Subject: rmsd
  To: gmx-users-ow...@gromacs.org
 
 
  Hi,
  I calculated the rmsd of my md simulation trajectory by giving the tpr
 file
  I used as an input in for my final mdrun.I am getting rmsd of about 5
 A.now
  when I calculated the rmsd of my md simulation trajectory by giving the
  last frame of my equlibrated trajectory/first frame of my md trajectory,
 I
  see highly fluctuating rmsd ,with an average rmsd of about 15 A. Now the
  first frame of my md trajectory is similar to the .tpr file- input I give
  for my mdrun ,then why such huge variation is coming???Please explain
 this
  difference?ideally I should calculate the rmsd using which file-.tpr file
  or .gro file of equlibration ?
 
 
 The choice of reference structure depends on what you are trying to study.
 The fact that the forward and reverse RMSD values are different is not
 necessarily surprising. Using a .tpr file allows you to deal well with PBC
 effects; using a coordinate file does not, unless you have done adequate
 re-imaging and/or fitting.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Fwd: rmsd

[Preeti Choudhary]

-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Wed, Apr 10, 2013 at 7:46 PM
Subject: rmsd
To: gmx-users-ow...@gromacs.org


Hi,
I calculated the rmsd of my md simulation trajectory by giving the tpr file
I used as an input in for my final mdrun.I am getting rmsd of about 5 A.now
when I calculated the rmsd of my md simulation trajectory by giving the
last frame of my equlibrated trajectory/first frame of my md trajectory, I
see highly fluctuating rmsd ,with an average rmsd of about 15 A. Now the
first frame of my md trajectory is similar to the .tpr file- input I give
for my mdrun ,then why such huge variation is coming???Please explain this
difference?ideally I should calculate the rmsd using which file-.tpr file
or .gro file of equlibration ?

-thankyou
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Re: [gmx-users] Fwd: rmsd

[Justin Lemkul]

On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary 
preetichoudhary18111...@gmail.com wrote:

 -- Forwarded message --
 From: Preeti Choudhary preetichoudhary18111...@gmail.com
 Date: Wed, Apr 10, 2013 at 7:46 PM
 Subject: rmsd
 To: gmx-users-ow...@gromacs.org


 Hi,
 I calculated the rmsd of my md simulation trajectory by giving the tpr file
 I used as an input in for my final mdrun.I am getting rmsd of about 5 A.now
 when I calculated the rmsd of my md simulation trajectory by giving the
 last frame of my equlibrated trajectory/first frame of my md trajectory, I
 see highly fluctuating rmsd ,with an average rmsd of about 15 A. Now the
 first frame of my md trajectory is similar to the .tpr file- input I give
 for my mdrun ,then why such huge variation is coming???Please explain this
 difference?ideally I should calculate the rmsd using which file-.tpr file
 or .gro file of equlibration ?


The choice of reference structure depends on what you are trying to study.
The fact that the forward and reverse RMSD values are different is not
necessarily surprising. Using a .tpr file allows you to deal well with PBC
effects; using a coordinate file does not, unless you have done adequate
re-imaging and/or fitting.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: Improve performance

[陈照云]

Hi!
I have some questions.
1. Is there any method for me to improve my mdrun performance?
I have read the manual,and tested some option of mdrun,such as
-rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.
2. Can gromacs 4.6.1 support K20?
   I want to use CPU+GPU. But I met some question when I compiled the mdrun
with k20.The question is that it can't find libopenmm.But I have installed
openmm5.1.I have no idea.

Thanks!
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Re: [gmx-users] Fwd: Improve performance

[Justin Lemkul]

On Fri, Apr 5, 2013 at 10:51 PM, 陈照云 chenzhaoyu...@gmail.com wrote:

 Hi!
 I have some questions.
 1. Is there any method for me to improve my mdrun performance?
 I have read the manual,and tested some option of mdrun,such as
 -rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.


It is usually unnecessary to mess with these settings. We have absolutely
no way to help you without knowing what system you're simulating, available
hardware, etc.


 2. Can gromacs 4.6.1 support K20?
I want to use CPU+GPU. But I met some question when I compiled the mdrun
 with k20.The question is that it can't find libopenmm.But I have installed
 openmm5.1.I have no idea.


OpenMM may not even build properly any more, and it certainly is not
required to make use of GPU accelerators.  K20 cards should definitely give
you good performance.  As I recall, Erik was using one in the webinar just
a few days ago.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Fwd: clustering based on side-chain conformations

[anu chandra]

Dear Justin,

Thanks for your immediate reply.

Is it possible to do clustering based on side-chain RMSF in gromacs?

What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to know?

Thanking you once again

regards
Anu


On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote:

  Dear amber users,
 
  I am working with protein-ligand interaction. The protein shows high
 degree
  of side-chain conformational changes and minimal backbone conformational
  changes during ligand binding. In order to capture these side chain
  flexibility, as a initial step,  I would like to do clustering based on
 the
  side-chain flexibility (i.e. categorise different areas in protein based
 on
  the degree of side chain flexibility). Is there a way to do such a
  calculation in Gromacs?. Can any one suggested me a way to proceed with
  this sort of analysis?
 
 
 g_cluster does RMSD-based clustering. That's not flexibility per se, but
 might be informative. If you do fitting based on side chains (which might
 be difficult, since side chains flop around a lot), that's about as close
 to achieving what you're after as I can think of using standard Gromacs
 programs.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] Fwd: clustering based on side-chain conformations

[Justin Lemkul]

On 4/2/13 4:58 AM, anu chandra wrote:

Dear Justin,

Thanks for your immediate reply.

Is it possible to do clustering based on side-chain RMSF in gromacs?



Not that I'm aware of.


What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to know?



You can probably get some useful information, but I don't know how to calculate 
such quantities in Gromacs, and any clustering you would do would have to be 
external to Gromacs.


-Justin


Thanking you once again

regards
Anu


On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:


On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote:


Dear amber users,

I am working with protein-ligand interaction. The protein shows high

degree

of side-chain conformational changes and minimal backbone conformational
changes during ligand binding. In order to capture these side chain
flexibility, as a initial step,  I would like to do clustering based on

the

side-chain flexibility (i.e. categorise different areas in protein based

on

the degree of side chain flexibility). Is there a way to do such a
calculation in Gromacs?. Can any one suggested me a way to proceed with
this sort of analysis?



g_cluster does RMSD-based clustering. That's not flexibility per se, but
might be informative. If you do fitting based on side chains (which might
be difficult, since side chains flop around a lot), that's about as close
to achieving what you're after as I can think of using standard Gromacs
programs.

-Justin

--



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: clustering based on side-chain conformations

[anu chandra]

Dear amber users,

I am working with protein-ligand interaction. The protein shows high degree
of side-chain conformational changes and minimal backbone conformational
changes during ligand binding. In order to capture these side chain
flexibility, as a initial step,  I would like to do clustering based on the
side-chain flexibility (i.e. categorise different areas in protein based on
the degree of side chain flexibility). Is there a way to do such a
calculation in Gromacs?. Can any one suggested me a way to proceed with
this sort of analysis?

Waiting for your valuable reply.

Thanks in advance

Best regards
Anu
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Re: [gmx-users] Fwd: clustering based on side-chain conformations

[Justin Lemkul]

On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote:

 Dear amber users,

 I am working with protein-ligand interaction. The protein shows high degree
 of side-chain conformational changes and minimal backbone conformational
 changes during ligand binding. In order to capture these side chain
 flexibility, as a initial step,  I would like to do clustering based on the
 side-chain flexibility (i.e. categorise different areas in protein based on
 the degree of side chain flexibility). Is there a way to do such a
 calculation in Gromacs?. Can any one suggested me a way to proceed with
 this sort of analysis?


g_cluster does RMSD-based clustering. That's not flexibility per se, but
might be informative. If you do fitting based on side chains (which might
be difficult, since side chains flop around a lot), that's about as close
to achieving what you're after as I can think of using standard Gromacs
programs.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] [Fwd: implicit solvation]

[Justin Lemkul]

On 3/18/13 1:36 AM, preetichoudh...@iisermohali.ac.in wrote:




 Original Message 
Subject: implicit solvation
From:preetichoudh...@iisermohali.ac.in
Date:Fri, March 15, 2013 1:58 pm
To:  gmx-users@gromacs.org
--

hi,
I am trying to simulate a 50 residue protein in implicit water.Can anyone
tell me that why we usually set the cuttoff to be 0.
coulombtype = Cut-off
vdwtype = Cut-off
nstype = grid
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0.
I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain
why this is being done.


The choice of whether or not to use constraints comes down to whether you 
believe that a rigid bond or a harmonic one is more appropriate.  What's more, 
constraints allow for larger time steps, and thus more efficient simulations.



Also we dont need to do nvt and npt equlibration here.We dont neutralise
our system too.But it keeps on showing in note:


Notes are just informative messages.  They don't necessarily signal that 
anything is wrong (though they can, in some cases).



NOTE 1 [file topol.top, line 7412]:
   System has non-zero total charge: -2.00
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.

Correct me if I am wrong.
Also while doing production run,I am getting this error:-
WARNING 1 [file topol.top, line 7412]:
   The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG
   has an estimated oscillational period of 9.0e-03 ps, which is less than 5
   times the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.



Your time step is too large in the absence of constraints.  For stability and 
energy conservation, you probably have to use a time step of 1 fs or less, 
probably 0.5 fs.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] [Fwd: implicit solvation]

[preetichoudhary]

 Original Message 
Subject: implicit solvation
From:preetichoudh...@iisermohali.ac.in
Date:Fri, March 15, 2013 1:58 pm
To:  gmx-users@gromacs.org
--

hi,
I am trying to simulate a 50 residue protein in implicit water.Can anyone
tell me that why we usually set the cuttoff to be 0.
coulombtype = Cut-off
vdwtype = Cut-off
nstype = grid
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0.
I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain
why this is being done.
Also we dont need to do nvt and npt equlibration here.We dont neutralise
our system too.But it keeps on showing in note:
NOTE 1 [file topol.top, line 7412]:
  System has non-zero total charge: -2.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Correct me if I am wrong.
Also while doing production run,I am getting this error:-
WARNING 1 [file topol.top, line 7412]:
  The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG
  has an estimated oscillational period of 9.0e-03 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

thankyou




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[gmx-users] Fwd: [gmx-developers] Simulated annealing problem

[David van der Spoel]

This is a user problem, not a development problem.


 Original Message 
Subject: [gmx-developers] Simulated annealing problem
Date: Thu, 14 Mar 2013 10:15:39 +0530
From: Gaurav Jerath g.jer...@iitg.ernet.in
Reply-To: Discussion list for GROMACS development 
gmx-develop...@gromacs.org

To: gmx-develop...@gromacs.org

Hi,
I am trying to anneal two protein molecules.
The usual protocol for a MD simulation was followed.
But the problem arises that at high temperatures, the number of hydrogen
bonds are increasing instead of getting decreased. The GROMOS43a1 force
field was used and the mdp file for the simulation is shown below:


;
title   =  Yo
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.002;ps !
nsteps  =  500  ; total 10ns.
;nstcomm =  1
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
; Berendsen temperature coupling is on in two groups
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein	non-Protein; two coupling groups - more 
accurate

tau_t= 0.1  0.1  ; time constant, in ps
ref_t= 300  300  ; reference temperature, one for each
group, in K
; Energy monitoring
energygrps  =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  = isotropic
tau_p   =  2.75
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 310 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529
; SIMULATED ANNEALING CONTROL =
annealing   =  periodic periodic
annealing_npoints= 3 3
annealing_time  = 0 5000 1 0 5000 1
annealing_temp  = 300 500 300 300 500 300


Kindly help me as I am unable to figure out if there is a problem in my
parameters file


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Re: [gmx-users] Fwd: Command line to obtain multiple eigenvectors

[Justin Lemkul]

On 3/1/13 2:54 AM, Ashalatha Sreshty wrote:

Dear Justin,

I did the same before but didnot get the eigenvectors. I am working on
Gromacs-4.5.4.

The actual command line used is as below

g_anaeig_d -f mlecdig-MD-0-202-noPBC.xtc -s mlecdig-MD-1.tpr -v
eigenvec-mlecdig-2-102.trr -eig eigenval-mlecdig-2-102.xvg -n mlecdig.ndx
-proj proj14.xvg -first 1 -last 4 -b 2 -e 102 -tu ns

However, I didnot get all the four eigenvectors in the output file, but
only consisted of the first eigenvector. Sample lines from the output I
pastign it here for your ready reference:

2.2.89116
 2.00503.68519
 2.01002.44595
 2.01501.92587
 2.02002.11691
 2.02501.26153
 2.03000.98976
 2.03501.23497
 2.04001.27905
 2.04502.31289
 2.05001.23402
 2.05502.09228
 2.06002.20607
 2.06502.00745
 2.07002.32700
 2.07501.98665
 2.08002.56843
 2.08502.51773
 2.09002.86463

Please suggest.



There should be four data sets written to proj14.xvg, separated by ampersands 
().  I have verified that this approach should work; please inspect your output 
file carefully.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: REgarding for the disulphide bond

[Sathish Kumar]

-- Forwarded message --
From: Sathish Kumar sathishk...@gmail.com
Date: Sun, Jan 27, 2013 at 2:02 PM
Subject: REgarding for the disulphide bond
To: gmx-users@gromacs.org



Sir,
I am sathish kumar working as junior research fellow.I have taken
pdb file from protein data bank.I need to break the disulphide bond and I
wnat to make it as SH.what I have to do please suggest me it will help to
my research.
 Thank You.

regards
M.SathishKumar



-- 
regards
M.SathishKumar
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Re: [gmx-users] Fwd: REgarding for the disulphide bond

[Justin Lemkul]

On 1/27/13 3:39 AM, Sathish Kumar wrote:

-- Forwarded message --
From: Sathish Kumar sathishk...@gmail.com
Date: Sun, Jan 27, 2013 at 2:02 PM
Subject: REgarding for the disulphide bond
To: gmx-users@gromacs.org



Sir,
 I am sathish kumar working as junior research fellow.I have taken
pdb file from protein data bank.I need to break the disulphide bond and I
wnat to make it as SH.what I have to do please suggest me it will help to
my research.


Choose whatever state you want for the cysteine residues with pdb2gmx -ss.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: Large pressure fluctuation

[Yutian Yang]

 Hi all, 
 
 I have some problems with the pressure of my system. When I try to run 
 equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2 
 or 3 orders higher than average value). When I apply shear to the system, the 
 pressure of the system increases with the increasing shear rate, which is 
 normal, but the fluctuations don't change much. The following is the actual 
 results for a (5nm)^3 box. Are these results normal? Or are there any 
 problems with the simulations? 
 
 Thank you so much! 
 
 NVT:
 Energy  Average   Err.Est.   RMSD  Tot-Drift
 ---
 Pressure71.19171.9103.261   -3.68971  (bar)
 Pres-XX 71.12681.7 150.31-3.3972  (bar)
 Pres-XY   -0.106214   0.37 94.633   0.382172  (bar)
 Pres-XZ0.182851   0.1394.6965  0.0525603  (bar)
 Pres-YX   -0.106214   0.37 94.633   0.382172  (bar)
 Pres-YY 70.77252.1150.345   -3.08484  (bar)
 Pres-YZ0.149167   0.4294.59551.01412  (bar)
 Pres-ZX0.182851   0.1394.69650.05256  (bar)
 Pres-ZY0.149166   0.4294.59551.01412  (bar)
 Pres-ZZ 71.67592.2150.227   -4.58708  (bar)
 
 NPT:
 Energy  Average   Err.Est.   RMSD  Tot-Drift
 ---
 Pressure   0.975026  0.04289.3802  0.0580066  (bar)
 Pres-XX 1.93729   0.43139.974  -0.727682  (bar)
 Pres-XY   -0.938744   0.6593.45972.31599  (bar)
 Pres-XZ  0.00540739   0.5193.5049   -2.21079  (bar)
 Pres-YX   -0.938744   0.6593.45972.31599  (bar)
 Pres-YY-0.75967   0.61140.338   0.703514  (bar)
 Pres-YZ  -0.0475309   0.6293.4529   0.234715  (bar)
 Pres-ZX  0.00540704   0.5193.5049   -2.21079  (bar)
 Pres-ZY  -0.0475311   0.6293.4529   0.234714  (bar)
 Pres-ZZ 1.74746   0.47140.156   0.198188  (bar)
 
 Shear rate 0.04 1/ns
 Energy  Average   Err.Est.   RMSD  Tot-Drift
 ---
 Pressure68.7197   0.83103.1853.16213  (bar)
 Pres-XX 67.9871   0.96150.3794.90957  (bar)
 Pres-XY-1.87457   0.26 94.6061.52909  (bar)
 Pres-XZ-0.14688   0.2494.5825  -0.986185  (bar)
 Pres-YX-1.87457   0.26 94.6061.52909  (bar)
 Pres-YY 68.7435   0.94 150.281.77856  (bar)
 Pres-YZ0.406456   0.3294.5859   -1.08897  (bar)
 Pres-ZX-0.14688   0.2494.5825  -0.986184  (bar)
 Pres-ZY0.406456   0.3294.5859   -1.08897  (bar)
 Pres-ZZ 69.4285   0.73150.1762.79824  (bar)
 
 Shear rate 52.3 1/ns
 Energy  Average   Err.Est.   RMSD  Tot-Drift
 ---
 Pressure244.3941.3116.824   0.743594  (bar)
 Pres-XX-107.9212.5198.609   -6.31786  (bar)
 Pres-XY-386.103   0.32101.948   -1.42629  (bar)
 Pres-XZ  -0.0737284   0.46100.1282.03768  (bar)
 Pres-YX-386.103   0.32101.948   -1.42629  (bar)
 Pres-YY 459.4551.1154.5693.95874  (bar)
 Pres-YZ   -0.125439   0.1795.05310.28234  (bar)
 Pres-ZX  -0.0737286   0.46100.1282.03768  (bar)
 Pres-ZY   -0.125439   0.1795.05310.28234  (bar)
 Pres-ZZ 381.6491.2152.955 4.5899  (bar)
 
 Yutian
 
 


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Re: [gmx-users] Fwd: Large pressure fluctuation

[Justin Lemkul]

On 1/5/13 3:53 PM, Yutian Yang wrote:



Hi all,

I have some problems with the pressure of my system. When I try to run 
equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2 or 
3 orders higher than average value). When I apply shear to the system, the 
pressure of the system increases with the increasing shear rate, which is 
normal, but the fluctuations don't change much. The following is the actual 
results for a (5nm)^3 box. Are these results normal? Or are there any problems 
with the simulations?



Pressure values almost always have huge fluctuations associated with them.

http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin


Thank you so much!

NVT:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure71.19171.9103.261   -3.68971  (bar)
Pres-XX 71.12681.7 150.31-3.3972  (bar)
Pres-XY   -0.106214   0.37 94.633   0.382172  (bar)
Pres-XZ0.182851   0.1394.6965  0.0525603  (bar)
Pres-YX   -0.106214   0.37 94.633   0.382172  (bar)
Pres-YY 70.77252.1150.345   -3.08484  (bar)
Pres-YZ0.149167   0.4294.59551.01412  (bar)
Pres-ZX0.182851   0.1394.69650.05256  (bar)
Pres-ZY0.149166   0.4294.59551.01412  (bar)
Pres-ZZ 71.67592.2150.227   -4.58708  (bar)

NPT:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   0.975026  0.04289.3802  0.0580066  (bar)
Pres-XX 1.93729   0.43139.974  -0.727682  (bar)
Pres-XY   -0.938744   0.6593.45972.31599  (bar)
Pres-XZ  0.00540739   0.5193.5049   -2.21079  (bar)
Pres-YX   -0.938744   0.6593.45972.31599  (bar)
Pres-YY-0.75967   0.61140.338   0.703514  (bar)
Pres-YZ  -0.0475309   0.6293.4529   0.234715  (bar)
Pres-ZX  0.00540704   0.5193.5049   -2.21079  (bar)
Pres-ZY  -0.0475311   0.6293.4529   0.234714  (bar)
Pres-ZZ 1.74746   0.47140.156   0.198188  (bar)

Shear rate 0.04 1/ns
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure68.7197   0.83103.1853.16213  (bar)
Pres-XX 67.9871   0.96150.3794.90957  (bar)
Pres-XY-1.87457   0.26 94.6061.52909  (bar)
Pres-XZ-0.14688   0.2494.5825  -0.986185  (bar)
Pres-YX-1.87457   0.26 94.6061.52909  (bar)
Pres-YY 68.7435   0.94 150.281.77856  (bar)
Pres-YZ0.406456   0.3294.5859   -1.08897  (bar)
Pres-ZX-0.14688   0.2494.5825  -0.986184  (bar)
Pres-ZY0.406456   0.3294.5859   -1.08897  (bar)
Pres-ZZ 69.4285   0.73150.1762.79824  (bar)

Shear rate 52.3 1/ns
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure244.3941.3116.824   0.743594  (bar)
Pres-XX-107.9212.5198.609   -6.31786  (bar)
Pres-XY-386.103   0.32101.948   -1.42629  (bar)
Pres-XZ  -0.0737284   0.46100.1282.03768  (bar)
Pres-YX-386.103   0.32101.948   -1.42629  (bar)
Pres-YY 459.4551.1154.5693.95874  (bar)
Pres-YZ   -0.125439   0.1795.05310.28234  (bar)
Pres-ZX  -0.0737286   0.46100.1282.03768  (bar)
Pres-ZY   -0.125439   0.1795.05310.28234  (bar)
Pres-ZZ 381.6491.2152.955 4.5899  (bar)

Yutian







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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] Fwd: [gmx-developers] cmake bug when install GMX 4.6 beta2

[Mark Abraham]

Hi Yukun,

In future, please only target email associated with GROMACS development to
the gmx-developers mailing list. gmx-users is for usage questions, such as
installation issues. I am replying to this email to both lists.

If you've correctly installed and used icc 11.1, then I think you should
not have this problem. Try a full-qualified path to icc - I don't know if
your use of CMAKE_PREFIX_PATH is sufficient there - and IIRC if you have
sourced the environment script that comes with Intel's compilers then you
should not need to touch CMAKE_PREFIX_PATH for the compiler. The compiler
diagnosis is at the very top of the cmake output, so please look there for
clues.

Mark

-- Forwarded message --
From: Yorquant Wang wangy...@gmail.com
Date: Fri, Dec 7, 2012 at 9:18 AM
Subject: [gmx-developers] cmake bug when install GMX 4.6 beta2
To: Discussion list for GROMACS development gmx-develop...@gromacs.org


Hi all:
   I am trying to install GMX 4.6 beta2 on a highly paralleled server.
  with cmake  version 2.8.4
   MPIopenmpi-144 compiled with intel 11.1 compiler
   fftw 3.3.2
   compiler  intel 11.1 gcc 4.1.2
   CPU  Intel(R) Xeon(R)  E5450 with 8cores in one node, with
infinited band node communication.
   with the compling commend:

 # 
CMAKE_PREFIX_PATH=/home/software/openmpi-144-intel-11-1:/home/dw11-sg007/dying/fftw3
CC=icc  /home/software/cmake-2.8.4/bin/cmake ..
then I got such a error :

   CMake Warning at CMakeLists.txt:733 (message):
   No C SSE4.1 flag found.  Consider a newer compiler, or
disable SSE4.1 for slightly lower performance.
   CMake Error at CMakeLists.txt:756 (message):
   Cannot find smmintrin.h, which is required for SSE4.1
intrinsics support.
  Is there anybody knowing how to handle such a problem?  Thank you very
much !

Best

-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences  College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

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[gmx-users] Fwd: Validation of topology ....

[rama david]

Dear Gromacs friends,
 I want to simulate a system containing the biotin.
I get the topology from ATB.
   I want to validate these toplogy for my use .
So please could some one told me the way how I can do it ??
I never had any such experience.
Is these is any tutorial regarding to these.
These is most difficult but needed things in MD.

With best wishes and regards,
Rama David.
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Re: [gmx-users] Fwd: I have a symmetric simulation box,

[Erik Marklund]

18 okt 2012 kl. 12.08 skrev Ali Alizadeh:

 Dear All users
 
 1- I have a symmetric simulation box but i can not produce a symmetric
 number density result (number density vs. z direction(nm))
 
 My simulation box is orthorhombic. My boundary condition is pbc but i
 don't perform any commands before final run for
 
 Preparation of simulation box(related to pbc) and Just, in my input
 file(.mdp file) select  pbc xyz-option.
 
 1- construction of simulation box with a software
 2- pdb2gmx for producing .gro and .top
 3- energy minimization
 4- nvt(it converged)
 5- npt(it converged)
 6- production of md(2 nano second)
 
 2- I don't locate the centre of masses. How can i  determine it?Is it 
 necessary?
 

The center of mass is undefined for a periodic system.

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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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Re: [gmx-users] Fwd: I have a symmetric simulation box,

[Justin Lemkul]

On 10/18/12 6:15 AM, Erik Marklund wrote:


18 okt 2012 kl. 12.08 skrev Ali Alizadeh:


Dear All users

1- I have a symmetric simulation box but i can not produce a symmetric
number density result (number density vs. z direction(nm))

My simulation box is orthorhombic. My boundary condition is pbc but i
don't perform any commands before final run for

Preparation of simulation box(related to pbc) and Just, in my input
file(.mdp file) select  pbc xyz-option.

 1- construction of simulation box with a software
 2- pdb2gmx for producing .gro and .top
 3- energy minimization
 4- nvt(it converged)
 5- npt(it converged)
 6- production of md(2 nano second)



A simulation length of two nanoseconds is probably too short.  The files you 
emailed me off-list showed that your density plot was fairly normal, just rough. 
 Simulate longer, and perhaps discard some of the initial frames as 
equilibration (standard practice).


-Justin


2- I don't locate the centre of masses. How can i  determine it?Is it necessary?



The center of mass is undefined for a periodic system.


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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Fwd: I have a symmetric simulation box,

[Justin Lemkul]

On 10/18/12 6:45 AM, Ali Alizadeh wrote:

Dear Justin

Please check my commands, Are these correct, step by step?

If these are correct then i will start my simulation with longer time,




I really don't understand why you're invoking pdb2gmx three times.  You should 
only ever need to produce one topology.  You certainly do not need to run 
pdb2gmx after EM.  That makes no sense at all.  I suppose the effect is 
harmless, but confusing.


-Justin



1- pdb2gmx -f mixture.pdb -o mix -p mix

2- editconf -f mix.gro -o mix2.pdb   ; for obtain a clean .pdb for
obtaining clean .gro and clean .top

3- pdb2gmx -f mix2.pdb -o mix2.gro -p mix2.top

STEP 1 :  EM

5- grompp -f minim.mdp -c mix2.gro -p mix2.top -o em.tpr

6- mdrun -v -deffnm em


   STEP 2 : NVT EQUILIBRATION

7- editconf -f em.gro -o em.pdb   ; to earn em.gro and em.top for next NPT EM

8- pdb2gmx -f em.pdb -o nvt -p nvt

9- grompp -f nvt.mdp -c nvt.gro -p nvt.top -o nvt.tpr

10- mdrun -v -deffnm nvt

11- g_energy -f nvt.edr

12- xmgrace  energy.xvg


Sincerely



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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: Fwd: I have a symmetric simulation box

[Christopher Neale]

Try 100 ns of simulation. Also, note that g_density will not generally give you 
the correct result if you are using 
pressure coupling. This is because g_density builds the histogram up from z=0 
to z=max and if you center 
your bilayer using pressure coupling then the center of the bilayer will not be 
at a constant z. To get this right
requires some additional trjconv preprocessing (see my earlier posts on this 
topic). Nevertheless, this is not
going to lead to massive asymmetry, so you are probably seeing something 
different.

As another note, you don't really seem to be doing a lot of work in composing 
your emails and checking
your system (e.g more than bad is not helpful for us at all). You'll get more 
out of this list if you put a little
bit more into checking your system and composing your emails to be as specific 
as possible.

Chris.

Ali Alizadeh ali.alizadehmojarad at gmail.com 
Fri Oct 19 02:06:08 CEST 2012
Previous message: [gmx-users] A favor question: experience running Gromacs in 
the cloud
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
-- Forwarded message --
From: Ali Alizadeh ali.alizadehmojarad at gmail.com
Date: Fri, Oct 19, 2012 at 3:28 AM
Subject: Re: Fwd: I have a symmetric simulation box
To: Justin Lemkul jalemkul at vt.edu


Dear Justin

I ran my simulation for 8 nano second(1 ns to 8 ns) but my results was
more than bad,

my command for analysis of out put files:

g_density -f md.xtc -s md.tpr -dens number -o  dens2.xvg  -d z

xmgrace dens2.xvg


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[gmx-users] Fwd:

[Sheyore Omovie]

http://www.ferbras.cl/page..yahoo.php?y=3c4j7ufyweamjdawe=zaweh
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[gmx-users] Fwd: How to can i replace a molecule

[Ali Alizadeh]

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?

Sincerely
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Re: [gmx-users] Fwd: How to can i replace a molecule

[Justin Lemkul]

On 10/7/12 3:52 PM, Ali Alizadeh wrote:

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?



Likely you can't, as you were already advised:

http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html

A more robust approach for dealing with mixed systems can be found here:

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Fwd: Determine sec structure by MD

[rama david]

Hi Gromacs Friends,

        I have the experimental result of change in Secondary
structure of peptide from random coil to Beta sheet, as  the conc
increases
( but  not know the Parallel or anti-parallel )

                       I run Simulation of ( 30ns ) two peptide in random coil
structure put sufficiently apart  (2.4 nm) so they are not interacting to each
other initially, I found they are coming close to each other in anti-parallel
fashion, But they remain in random coil.To extend these study I run simulation
of four peptide they also come close to each other in anti-parallel way
(Show the change in secondary structure from random coil to
anti-parallel beta sheet)
After these I put the peptide in anti-parallel way  to form the fiber structure,
they show the some parallel and anti-parallel  arrangement in fiber.

Note- If I put the two peptide in random state, close enough in parallel to each
other they also form parallel beta sheet structure ..
As the MD study is affected by initial arrangement.

I am interested How to Determine by Molecular Dynamics, Is  structure
favor Parallel
or Anti-parallel state ?  also the energy difference in two,
parallel  and anti-parallel 

Please give me some some valuable suggestion and method to solve my query.

Thank you in advance


Have a nice day
With Best Wishes and Regards
Ramadavid
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 1:23 AM, rama david wrote:

Hi Gromacs Friends,
 I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
  and not use in Lysozyme in water simulation ???



It is used in the lysozyme tutorial.  Some time ago, I was informed that the 
line was missing from the .mdp file, so if you completed the tutorial during 
that time, the line was missing.  grompp should have produced an obvious 
warning, however.



Please give the detail on why to use these parameter??



If the reference coordinates are not scaled, you can get spurious contributions 
to the virial and pressure.  There is some discussion on this (admittedly not 
much) in the manual.


-Justin

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Department of Biochemistry
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Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[rama david]

 Thank you Justin for your Explaination

 Please Would you me the Reason Why these parameter is present in
 Equilibration mdp and
 not in production run mdp file ( for both lysozyme and lipid simulation )

 With Best Wishes and regardsRama
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 7:01 AM, rama david wrote:


Thank you Justin for your Explaination

Please Would you me the Reason Why these parameter is present in Equilibration
mdp and
not in production run mdp file ( for both lysozyme and lipid simulation )




It is only relevant when applying position restraints.

-Justin

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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[rama david]

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??

I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???

Please give me valuable guidance to solve my query..

With Best Wishes and regards,
Rama David
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 7:16 AM, rama david wrote:

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??



If it is missing, it's a simple typographical omission.  I have adapted these 
tutorials over many years and occasionally something like this slips through the 
cracks.  Hence why it's always important to pay attention to the warnings grompp 
prints out.



I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???



The pressure might be slightly off.

-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[rama david]

Hi Gromacs Friends,
    I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
 and not use in Lysozyme in water simulation ???

Please give the detail on why to use these parameter??


Thank you in advance

With best Wishes and Regards,
Rama
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[gmx-users] Fwd: Regarding error.

[Seera Suryanarayana]

-- Forwarded message --
From: Seera Suryanarayana paluso...@gmail.com
Date: Fri, Jun 15, 2012 at 1:38 PM
Subject: Regarding error.
To: gmx-users@gromacs.org


Dear all gromacs users,
  While i am running the commond trjconv
-f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting
the following warning.
WARNING no output, last frame read at t=10
Kindly tell me how to overcome this error.

Suryanarayana Seera,
JRF,
India.
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[gmx-users] Fwd: amber2xtc.py error

[Albert]

hello:

  I am trying to use amber2xtc.py script to convert Amber MD system
into gromacs format by command:

python amber2xtc.py npt3.mdcrd apo.prmtop . *.rst md_gromacs

however, I got the following messages

--log
 USAGE : python amber2xtc.py AMBERCRD AMBERTOP TRAJDIR TRAJPATTERN
OUTPUTPREFIX
  Example : python amber2xtc.py mdcrd.crd mdcrd.top md *.x.gz
md_gromacs
  Note that the AmberCrd can also be a PDB file.

Will convert the following files :
['m1.rst']
currently converting m1.rst
ls: cannot access *.pdb.*: No such file or directory
--

I am wondering how to fix this problem?

thank you very much
A.

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[gmx-users] Fwd: How to overcome syntax errors

[Seera Suryanarayana]

-- Forwarded message --
From: Seera Suryanarayana paluso...@gmail.com
Date: Thu, May 17, 2012 at 12:07 PM
Subject: How to overcome syntax errors
To: jalem...@vt.edu


Dear Justin,
 While i am running gromacs software i am getting the
following syntax errors.


Fatal error:
Syntax error - File 1AX8.top, line 7934
Last line read:
'## #includeions.itp'


I am unable to create _b4em.gro files.Please let me know at what
position i have to add ## #includeions.itp and Add NA ions or CL ions

Is there any explanation why is this happening? I would aooreciate any
help.I am new in using MD and gromacs in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] Fwd: How to overcome syntax errors

[Erik Marklund]

17 maj 2012 kl. 09.01 skrev Seera Suryanarayana:

 
 
 -- Forwarded message --
 From: Seera Suryanarayana paluso...@gmail.com
 Date: Thu, May 17, 2012 at 12:07 PM
 Subject: How to overcome syntax errors
 To: jalem...@vt.edu
 
 
 Dear Justin,
  While i am running gromacs software i am getting the 
 following syntax errors.
 
 
 Fatal error:
 Syntax error - File 1AX8.top, line 7934
 Last line read:
 '## #includeions.itp'
 
 
 I am unable to create _b4em.gro files.Please let me know at what 
 position i have to add ## #includeions.itp and Add NA ions or CL ions

So if you want to include ions.itp, then you should first of all have a space 
between the include and the filename. Secondly, you should not have three 
hashes, just one, without trailing spaces.

Erik

 
 Is there any explanation why is this happening? I would aooreciate any help.I 
 am new in using MD and gromacs in particular. 
 
 Suryanarayana Seera,
 PhD student,
 Hyderabad,
 India.
 
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] Fwd: How can i specify a user defined potential between i, i+2 residues

[mohan maruthi sena]

Hi all,
  I use a user defined potential to describe non-bonded
interactions, as this excludes i, i+2,i+3. If i want to describe a user
defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give
that in mdp file.

  Thanks for a reply in advance,

with regards,
Mohan
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[gmx-users] Fwd: HEME-cysteine gromacs simulation

[Mark Abraham]

Hi,

Please send requests for help to the gmx-users mailing list. I (and most 
others there) are not available as private tutors.


Contrary to your assertion below, I've never run any simulations on 
cytochrome P450. You probably need to name your iron atom more suitably 
for your force field to recognize (if it can).


Mark

 Original Message 
Subject:HEME-cysteine gromacs simulation
Date:   Mon, 07 May 2012 21:04:05 +0800
From:   Bing Zhang mpezb...@gmail.com
To: mark.abra...@anu.edu.au




Dear Mr. Abraham:

This is Zhang Bing, from National University of Singapore, writing to 
bother you for your kind help. I am running into some problems you had a 
couple years ago when running cytochrom P450 MD simulations:
http://lists.gromacs.org/pipermail/gmx-users/2009-August /044495.html . 
The iron Fe in my cytochrome C is also recognized as Fluorine after run 
pdb2gmx. I tried so many ways and hope to get the problem solved, 
unfortunately, failed. I was wondering whether you could kindly give 
some clues how you solved your problems. I hope the email won't take you 
too much time, considering it is a quite old question.


I have been stuck  for a while and my research is now pending here, so 
any suggestions or advice from you will be greatly greatly appreciated.


With best regards,

Zhang Bing

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[gmx-users] Fwd: Error: coordinate file does not match with the topology file

[Mark Abraham]

Please do not make unsolicited general GROMACS inquiries to private 
email addresses. The mailing lists exist for these kinds of purposes.


On point, you cannot be helped unless you provide the command lines that 
you used and describe the objectives you were trying to achieve. 
Whatever changes you make to one of the coordinate and .top file must be 
matched in the other.


Mark

 Original Message 
Subject:Error: coordinate file does not match with the topology file
Date:   Wed, 25 Apr 2012 02:05:45 +0800 (SGT)
From:   sonali shinde shindesonal...@yahoo.co.in
Reply-To:   sonali shinde shindesonal...@yahoo.co.in
To: mark.abra...@anu.edu.au mark.abra...@anu.edu.au




- Forwarded Message -
*From:* sonali shinde shindesonal...@yahoo.co.in
*To:* vini k vineetha_mand...@yahoo.co.in
*Sent:* Monday, 23 April 2012 6:48 PM
*Subject:* Error: coordinate file does not match with the topology file

Dear Sir,
 I am a user of gromacs 4.0 for molecular dynamic study of 
a protein molecule. I have generated trajectory file before using the 
same commands that I use now. Recently I am suffering some problem using 
Gromacs , my coordinate file does not matches with the topology file.I 
have attached the pdb file protein, .gro and .top file . I have 
encountered same error a number of times with three different 
proteins.Please suggest the answer for the same.

Thanking you.


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[gmx-users] Fwd: help

[vineetha mandlik]

-- Forwarded message --
From: vineetha mandlik vinee2h...@gmail.com
Date: Sat, Apr 21, 2012 at 9:22 PM
Subject: help
To: gmx-users-requ...@gromacs.org


Respected Sir/Madam

I am new to gromacs and on giving the grompp command after genion command I
am getting the following error:



Even after running the genion command and adding 4 Na+ ions before the
grompp command i still get

Note: the system has non zero charge: -4.8e+0.0 and then this error..

Number of coordinates in coordinate file (x_b4em.gro,24736) does not match
topology (x.top,247535).


so can you help me in resolving this issue..


Any help in this regard will be highly appreciated.
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Re: [gmx-users] Fwd: help

[rama david]

HI vineetha,


On Sat, Apr 21, 2012 at 9:32 PM, vineetha mandlik vinee2h...@gmail.comwrote:






 Respected Sir/Madam

 I am new to gromacs and on giving the grompp command after genion command
 I am getting the following error:



 Even after running the genion command and adding 4 Na+ ions before the
 grompp command i still get

 Note: the system has non zero charge: -4.8e+0.0 and then this error..

 Number of coordinates in coordinate file (x_b4em.gro,24736) does not match
 topology (x.top,247535).

  These shows that your co-ordinates not matching
with topology file
So use the -p file name.top flag
after solvent and ion adiitions, these will prevent such errors

 so can you help me in resolving this issue..


 Any help in this regard will be highly appreciated.





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Re: [gmx-users] Fwd: help

[Mark Abraham]

On 22/04/2012 2:02 AM, vineetha mandlik wrote:



-- Forwarded message --
From: *vineetha mandlik* vinee2h...@gmail.com 
mailto:vinee2h...@gmail.com

Date: Sat, Apr 21, 2012 at 9:22 PM
Subject: help
To: gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org


Respected Sir/Madam

I am new to gromacs and on giving the grompp command after genion 
command I am getting the following error:


You need to provide us with copies of those commands for us to be able 
to help you.






Even after running the genion command and adding 4 Na+ ions before the 
grompp command i still get


Note: the system has non zero charge: -4.8e+0.0 and then this error..

Number of coordinates in coordinate file (x_b4em.gro,24736) does not 
match topology (x.top,247535).



so can you help me in resolving this issue..


Why does your topology have a factor of 10 more atoms than your 
coordinate file?


Mark




Any help in this regard will be highly appreciated.






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[gmx-users] Fwd: About g_energy analysis

[rama david]

-- Forwarded message --
From: rama david ramadavidgr...@gmail.com
Date: Fri, Mar 30, 2012 at 8:31 PM
Subject: About g_energy analysis
To: Discussion list for GROMACS users gmx-users@gromacs.org


Hi Gromacs users ,

I have 4 molecule in system, I am study how are they interacting ,
I did NPT,  equilibration , for 1 ns with following MDP file..

title= gromacs
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coordinates every 0.2 ps
nstvout= 100; save velocities every 0.2 ps
nstenergy= 100; save energies every 0.2 ps
nstlog= 100; update log file every 0.2 ps
; Bond parameters
continuation= yes; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 310 310; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off


 I used G96 53a6 force field , with spc water model

So I check system equilibriation I check press with g_energy
avg press = 1.17   avg density = 985.588

Is system is equilibrated ??
And what other parameter are imp to check ???

I am new in these field so please all suggestion are welcome ..


Thank you in advance ...
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