date:20111016

Re: [gmx-users] Simulation of membrane protein

2011-10-16 Thread Justin A. Lemkul

James Starlight wrote:

Justin, hello!

In the algorthm presented in the tutorial there is one inconvenience
that is many iterations of the shrinking/minimization of the protein (
e.g if i'd like to obrain good value for S per lipid for my structure).
Is there any way to make this process automated ? ( e.g some program
wich could do all of those operations untill defined value for some
magnitudes would be reached )

Sure, you could do all of it within a shell script that loops the commands and
checks the printed output.

Also I'd like to ask about g_membed. As I've understood for that program
I need in merged pdb struture ( consist of my peptide inserted in the
membrane ) as well as merged topology. Is there any way to prepare this
data exept the way presented in your tutorial ?
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)

That's what you obtain when concatenating the protein and membrane coordinate
files in my tutorial, prior to any inflation. You'd just have to add whatever
molecules are present in the [molecules] directive of the .top at that point.

E.g I've heard that this could also be done via PyMol. Where I could
find example of such preparation ?

I don't know of one.

-Justin

Thanks for your help,
James

2011/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>

James Starlight wrote:

Dear Gromacs's users!

I'd like to simulate some membrane proteins in their native
environment.

Recently I've found a good tutotial of the same simulation of
the KALP peptide in DPPC membrane

(http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html

Is there someone who have also tried to make thit tutorial ?

Yes, per our server logs, several hundred people have :)

First of all its very intresting for me the positioning of the
protein in the membrane via specific perl script called
infrategro. What values for the cutoff radius as well as
measurements of the area per lipid are most adequate for
different membrane proteins?

The ones given in the tutorial work quite well. They are the
defaults suggested by the developers of InflateGRO.

Could you also tell me some alternative ways of full algorithm
of the protein insertion in the membrane?

Careful use of genbox (but will require significantly more
equilibration as there will be large gaps), or g_membed.

-Justin

--
==__==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin

==__==
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mark Abraham


On 15/10/2011 9:02 PM, Mirco Wahab wrote:

On 10/15/2011 1:15 AM, Mark Abraham wrote:

I use

ccmake ..\
-DGMX_FFT_LIBRARY=mkl "\
-DMKL_LIBRARIES=${MKL}/lib/em64t/libmkl_intel_thread.so;${MKL}/lib/em64t/libmkl_lapack.so;${MKL}/lib/em64t/libmkl_core.so;${MKL}/lib/em64t/libmkl_em64t.a;${MKL}/lib/em64t/libguide.so;/usr/lib64/libpthread.so" 


\
-DMKL_INCLUDE_DIR=${MKL}/include\
-DGMX_MPI=ON\
-DGMX_THREADS=OFF


Thanks for your hints, I made it now through `cmake` with:

--- 8< --- [cut here] --

GMXVERSION=gromacs-4.5.5
GMXTARGET=/opt/gromacs455

MINC=/opt/intel/composerxe/mkl/include
MLIB=/opt/intel/composerxe/mkl/lib/intel64
ILIB=/opt/intel/composerxe/lib/intel64
LLIB=/usr/lib64

export CXX=icpc
export CC=icc

cmake ../$GMXVERSION  \
  -DGMX_FFT_LIBRARY=mkl
"-DMKL_LIBRARIES=${MLIB}/libmkl_intel_ilp64.so;${MLIB}/libmkl_core.so;${MLIB}/libmkl_intel_thread.so;${ILIB}/libiomp5.so;${LLIB}/libpthread.so"\ 


  -DMKL_INCLUDE_DIR=${MINC} \
  -DGMX_MPI=OFF \
  -DGMX_THREADS=ON  \
  -DCMAKE_INSTALL_PREFIX=${GMXTARGET}  \
  -DGMX_X11=OFF\
  -DGMX_BINARY_SUFFIX="_t"

---

on `make`, there are still some compiler flag related
problems. The cmake scripts invoked by the command
above identified the Intel64 compiler and guessed
'almost correct' optimization and code-generation options:
(Compiler: /opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/ic*)

--- [CMakeCache.txt] -

...

//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '

//Flags used by the compiler during release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG

//Flags used by the compiler during all build types
CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '

//Flags used by the compiler during release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG

...



These are obviously the wrong flags for the detected architecture,
sse2 is no longer available and so are the the mtune architectures.

The correct options for the actual compiler for Intel64 would read:

   CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
   CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG

   CMAKE_C_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99  '
   CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG


Even with the wrong options, the `make` would eventually succeed
with some option-warnings but without error.


Sure. GROMACS will not benefit noticeably from the SSE3 instruction set, 
so we don't bother looking for it.




But the install is broken. On `make install-mdrun`, the scripts would
remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
and bail out with the error below. Even if you copy the libraries
by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
before trying to link with them.

--- [cat errmsg.txt] -

[ 70%] Built target gmx
[ 89%] Built target md
[ 98%] Built target gmxpreprocess
[100%] Built target mdrun
[100%] Installing mdrun
-- Install configuration: "Release"
-- Install component: "libraries"
CMake Error at /x/y/Gromacs/build/src/gmxlib/cmake_install.cmake:38 
(FILE):

   file INSTALL cannot find
   
"/x/y/Gromacs/build/src/gmxlib/CMakeFiles/CMakeRelink.dir/libgmx.so.6".




Still broken with the new Intel Compiler but probably close ;-)


That looks very weird. What cmake version? What does make install-mdrun 
VERBOSE=1 say?


Mark
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[gmx-users] about the pulling

2011-10-16 Thread Tom

Dear Gromacs Users or Developers,

I am using the pulling the COM of object A towards B using:
-
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = yes
pull_ngroups = 1
pull_group0  = B
pull_group1  = A
pull_rate1   = -0.5714
pull_k1  = 5000
---
On the output file of pullx.xvg,  the sign of dZ
has been changed from negative to posivitve
or vice vrsa in all sudden. What does it mean?

The following is an example:

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"

---
173.74000.77622 8.14856
173.75000.77622 8.14897
173.76000.77622 8.14938
173.77000.77622 8.14977
173.78000.77622 -8.14987
173.79000.77622 -8.14954
173.80000.77622 -8.14924
173.81000.77622 -8.14895



Thanks a lot for the information!

Thanks,

Tom
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Re: [gmx-users] about the pulling

2011-10-16 Thread Justin A. Lemkul




Tom wrote:

Dear Gromacs Users or Developers,

I am using the pulling the COM of object A towards B using:
-
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = yes
pull_ngroups = 1
pull_group0  = B
pull_group1  = A
pull_rate1   = -0.5714
pull_k1  = 5000
---
On the output file of pullx.xvg,  the sign of dZ
has been changed from negative to posivitve
or vice vrsa in all sudden. What does it mean?



It means your pulled group is bouncing back and forth across a periodic 
boundary.  Use a larger box.  With distance geometry, the pulled distance must 
always be less than 1/2 the box vector in the pulled dimension(s).


-Justin


The following is an example:

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"

---
173.74000.77622 8.14856
173.75000.77622 8.14897
173.76000.77622 8.14938
173.77000.77622 8.14977
173.78000.77622 -8.14987
173.79000.77622 -8.14954
173.80000.77622 -8.14924
173.81000.77622 -8.14895



Thanks a lot for the information!

Thanks,

Tom


--


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


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[gmx-users] Fwd: about the pulling

2011-10-16 Thread Tom

Justin

you have good experience of pulling.

If you have time, please help with this publling problem:
abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!

i am pulling A object towards B along z-axis. But system
has pbc on x, y and z. Is it because of the pbc image of B
object that make grmx confused to report the sign.

In my system, A should be on the top of B in z-axis, but i just noticed
that at the intial step: 1dZ has been negative already.
It seems the system use the PBC image (in z-axis) of the reference object B
 to cacluate 1dZ, right?
--
@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  0.77622 -8.13474


Thanks a lot for the help!

Tom

-- Forwarded message --
From: Tom 
Date: Sun, 16 Oct 2011 23:02:09 +0800
Subject: about the pulling
To: gmx-users 

Dear Gromacs Users or Developers,

I am using the pulling the COM of object A towards B using:
-
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = yes
pull_ngroups = 1
pull_group0  = B
pull_group1  = A
pull_rate1   = -0.5714
pull_k1  = 5000
---
On the output file of pullx.xvg,  the sign of dZ
has been changed from negative to posivitve
or vice vrsa in all sudden. What does it mean?

The following is an example:

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"

---
173.74000.77622 8.14856
173.75000.77622 8.14897
173.76000.77622 8.14938
173.77000.77622 8.14977
173.78000.77622 -8.14987
173.79000.77622 -8.14954
173.80000.77622 -8.14924
173.81000.77622 -8.14895



Thanks a lot for the information!

Thanks,

Tom
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[gmx-users] Re: Fwd: about the pulling

2011-10-16 Thread Justin A. Lemkul




Tom wrote:

Justin

you have good experience of pulling.

If you have time, please help with this publling problem:
abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!



I already commented:

http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html


i am pulling A object towards B along z-axis. But system
has pbc on x, y and z. Is it because of the pbc image of B
object that make grmx confused to report the sign.



Likely.  If your box is not greater than about 16.3 nm in Z, then you'll have 
this problem.



In my system, A should be on the top of B in z-axis, but i just noticed
that at the intial step: 1dZ has been negative already.
It seems the system use the PBC image (in z-axis) of the reference object B
 to cacluate 1dZ, right?


Sounds right.

-Justin


--
@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  0.77622 -8.13474


Thanks a lot for the help!

Tom

-- Forwarded message --
From: Tom 
Date: Sun, 16 Oct 2011 23:02:09 +0800
Subject: about the pulling
To: gmx-users 

Dear Gromacs Users or Developers,

I am using the pulling the COM of object A towards B using:
-
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = yes
pull_ngroups = 1
pull_group0  = B
pull_group1  = A
pull_rate1   = -0.5714
pull_k1  = 5000
---
On the output file of pullx.xvg,  the sign of dZ
has been changed from negative to posivitve
or vice vrsa in all sudden. What does it mean?

The following is an example:

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"

---
173.74000.77622 8.14856
173.75000.77622 8.14897
173.76000.77622 8.14938
173.77000.77622 8.14977
173.78000.77622 -8.14987
173.79000.77622 -8.14954
173.80000.77622 -8.14924
173.81000.77622 -8.14895



Thanks a lot for the information!

Thanks,

Tom



--


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


--
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Please search the archive at 
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mirco Wahab


On 10/16/2011 2:25 PM, Mark Abraham wrote:

On 15/10/2011 9:02 PM, Mirco Wahab wrote:

On 10/15/2011 1:15 AM, Mark Abraham wrote:

I use
...

...
//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '

//Flags used by the compiler during release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG

//Flags used by the compiler during all build types
CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '

//Flags used by the compiler during release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG

...
These are obviously the wrong flags for the detected architecture,
sse2 is no longer available and so are the the mtune architectures.
The correct options for the actual compiler for Intel64 would read:
CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
with some option-warnings but without error.


Sure. GROMACS will not benefit noticeably from the SSE3 instruction set,
so we don't bother looking for it.


OK, I can understand that. But if the options (-mtune ***, -msse2)
are not longer available with the actual free Intel Compiler suites,
shouldn't the cmake definitions be adapted to this fact in order
to avoid loads of compiler warnings?


But the install is broken. On `make install-mdrun`, the scripts would
remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
and bail out with the error below. Even if you copy the libraries
by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
before trying to link with them.
...

That looks very weird. What cmake version? What does make install-mdrun
VERBOSE=1 say?


I'll attach the error messages err.msg, 5.9 KB).
 - cmake version 2.8.3
 - gcc 4.5.1 x64 (Linux) (20101208)

Thanks & regards

Mirco





/usr/bin/cmake -H/home/carlo/Gromacs/gromacs-4.5.5 -B/home/carlo/Gromacs/build 
--check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 install-mdrun
make[1]: Entering directory `/home/carlo/Gromacs/build'
/usr/bin/cmake -H/home/carlo/Gromacs/gromacs-4.5.5 -B/home/carlo/Gromacs/build 
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /home/carlo/Gromacs/build/CMakeFiles 68
make -f CMakeFiles/Makefile2 src/kernel/CMakeFiles/install-mdrun.dir/all
make[2]: Entering directory `/home/carlo/Gromacs/build'
make -f src/gmxlib/CMakeFiles/gmx.dir/build.make 
src/gmxlib/CMakeFiles/gmx.dir/depend
make[3]: Entering directory `/home/carlo/Gromacs/build'
cd /home/carlo/Gromacs/build && /usr/bin/cmake -E cmake_depends "Unix 
Makefiles" /home/carlo/Gromacs/gromacs-4.5.5 
/home/carlo/Gromacs/gromacs-4.5.5/src/gmxlib /home/carlo/Gromacs/build 
/home/carlo/Gromacs/build/src/gmxlib 
/home/carlo/Gromacs/build/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake 
--color=
make[3]: Leaving directory `/home/carlo/Gromacs/build'
make -f src/gmxlib/CMakeFiles/gmx.dir/build.make 
src/gmxlib/CMakeFiles/gmx.dir/build
make[3]: Entering directory `/home/carlo/Gromacs/build'
make[3]: Nothing to be done for `src/gmxlib/CMakeFiles/gmx.dir/build'.
make[3]: Leaving directory `/home/carlo/Gromacs/build'
/usr/bin/cmake -E cmake_progress_report /home/carlo/Gromacs/build/CMakeFiles  
14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61
[ 70%] Built target gmx
make -f src/mdlib/CMakeFiles/md.dir/build.make 
src/mdlib/CMakeFiles/md.dir/depend
make[3]: Entering directory `/home/carlo/Gromacs/build'
cd /home/carlo/Gromacs/build && /usr/bin/cmake -E cmake_depends "Unix 
Makefiles" /home/carlo/Gromacs/gromacs-4.5.5 
/home/carlo/Gromacs/gromacs-4.5.5/src/mdlib /home/carlo/Gromacs/build 
/home/carlo/Gromacs/build/src/mdlib 
/home/carlo/Gromacs/build/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color=
make[3]: Leaving directory `/home/carlo/Gromacs/build'
make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build
make[3]: Entering directory `/home/carlo/Gromacs/build'
make[3]: Nothing to be done for `src/mdlib/CMakeFiles/md.dir/build'.
make[3]: Leaving directory `/home/carlo/Gromacs/build'
/usr/bin/cmake -E cmake_progress_report /home/carlo/Gromacs/build/CMakeFiles  
85 86 87 88 89 90 91 92 93 94 95 96 97
[ 89%] Built target md
make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make 
src/kernel/CMakeFiles/gmxpreprocess.dir/depend
make[3]: Entering directory `/home/carlo/Gromacs/build'
cd /home/carlo/Gromacs/build && /usr/bin/cmake -E cmake_depends "Unix 
Makefiles" /home/carlo/Gromacs/gromacs-4.5.5 
/home/carlo/Gromacs/gromacs-4.5.5/src/kernel /home/carlo/Gromacs/build 
/home/carlo/Gromacs/build/src/kernel 
/home/carlo/Gromacs/build/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake
 --color=
make[3]: Leaving directory `/home/carlo/Gromacs/build'
make -f src/ker

[gmx-users] oops, s/gcc 4.5.1/icc 12.1.0/

2011-10-16 Thread Mirco Wahab


On 10/16/2011 10:04 PM, Mirco Wahab wrote:

- gcc 4.5.1 x64 (Linux) (20101208)


with the said gcc, all builds works fine, the problem
arises with the Intel suite (icc/icpc 12.1.0)

sorry for the typo.

M.
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[gmx-users] g_hbond frames

2011-10-16 Thread Yao Yao

Hi Gmxers,

I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs 
integration step but found the error,

"Cannot calculate autocorrelation of life times with less than two frames",

I am quite sure my system is just a regular protein in a cubic water box. 

And the size of trajectory is big with no error messages when finished.
So it should not be just a couple of frames. 

Anyone met this before?


Thanks,

Yao
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Re: [gmx-users] g_hbond frames

2011-10-16 Thread Justin A. Lemkul




Yao Yao wrote:

Hi Gmxers,

I ran g_hbond between my protein and water for a 3ns trajectory with 2 
fs integration step but found the error,


"Cannot calculate autocorrelation of life times with less than two frames",

I am quite sure my system is just a regular protein in a cubic water box.
And the size of trajectory is big with no error messages when finished.
So it should not be just a couple of frames.
Anyone met this before?



Without providing the exact command you used, there's little anyone can do to 
help.  In addition, you may want to run gmxcheck on your trajectory to make sure 
there are no corrupt frames.


-Justin


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


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[gmx-users] topologies for POPE and DMPE

2011-10-16 Thread Roy Lee

Dear all,



I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4,
and a forcefield of gromos96. However i don't have the topologies files for
lipid bilayer for POPE and DMPE. Anybody knows where can i get the
topologies file for POPE and DMPE ?



Any help is much appreciated.



Thanks a lot!



Roy
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mark Abraham


On 17/10/2011 7:04 AM, Mirco Wahab wrote:

On 10/16/2011 2:25 PM, Mark Abraham wrote:

On 15/10/2011 9:02 PM, Mirco Wahab wrote:

On 10/15/2011 1:15 AM, Mark Abraham wrote:

I use
...

...
//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '

//Flags used by the compiler during release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 
-DNDEBUG


//Flags used by the compiler during all build types
CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '

//Flags used by the compiler during release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG

...
These are obviously the wrong flags for the detected architecture,
sse2 is no longer available and so are the the mtune architectures.
The correct options for the actual compiler for Intel64 would read:
CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
with some option-warnings but without error.


Sure. GROMACS will not benefit noticeably from the SSE3 instruction set,
so we don't bother looking for it.


OK, I can understand that. But if the options (-mtune ***, -msse2)
are not longer available with the actual free Intel Compiler suites,
shouldn't the cmake definitions be adapted to this fact in order
to avoid loads of compiler warnings?


If someone can identify a way to detect old and new, free and non-free 
compiler suites then we might consider it. Reality is that GROMACS 
spends a heavy majority of its time in loops written mostly in assembly 
code (using SSE or SSE2 if applicable), or in the FFT library. Compiler 
performance makes a negligible contribution to performance of the rest, 
so it is really not worth while maintaining complex compiler tweaks.



But the install is broken. On `make install-mdrun`, the scripts would
remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
and bail out with the error below. Even if you copy the libraries
by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
before trying to link with them.
...

That looks very weird. What cmake version? What does make install-mdrun
VERBOSE=1 say?


I'll attach the error messages err.msg, 5.9 KB).
 - cmake version 2.8.3
 - gcc 4.5.1 x64 (Linux) (20101208)


With cmake 2.8.2 and icc 12.1.0 20110811 using the aforementioned flags, 
I get smooth installation of the git version of 4.5.5. Moreover, I don't 
even get


.../build/src/gmxlib/CMakeFiles/CMakeRelink.dir

being created. So I think there is something idiosyncratic about your 
tool chain that is at the root of this.


Mark
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[gmx-users] trjconv:solute at the center

2011-10-16 Thread Nilesh Dhumal

Hello,

I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.

trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center   -o 500-11.pdb

I tried to keep the solute at the center box. In visualization, the solute
is not at center , its close to box edges.

How can I keep the solute at the center.


I am using Gromacs 4.0.7 version.

Thanks

Nilesh










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[gmx-users] cyclosporine A

2011-10-16 Thread Алексей Раевский

Hi!
I need an advice concerninng topology building of such substance like
cyclosporine A. I've tried to make it with antechamber tool, cause I wanted
to use amber99sb forcefield. But the program gave me an error in the
begining and no results in the end after 12 hours of calculations ))) Can
you give any suggestions for my next steps? This compound is a peptide chain
built from acyl-adenylated amino acids (L-valine, L-leucine, L-alanine,
L-glycine, 2-aminobutyric acid, 4-methylthreonine, and D-alanine).
Thank you very much!

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Nemo me impune lacessit*
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Re: [gmx-users] Simulation of membrane protein

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[gmx-users] about the pulling

Re: [gmx-users] about the pulling

[gmx-users] Fwd: about the pulling

[gmx-users] Re: Fwd: about the pulling

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[gmx-users] oops, s/gcc 4.5.1/icc 12.1.0/

[gmx-users] g_hbond frames

Re: [gmx-users] g_hbond frames

[gmx-users] topologies for POPE and DMPE

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[gmx-users] trjconv:solute at the center

[gmx-users] cyclosporine A

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