Re: [gmx-users] reagarding polarisable force field in gromacs

[Mark Abraham]

On 20/12/2010 3:44 PM, sreelakshmi ramesh wrote:

Dear justin ,
I am using tip4p water model for my work and i 
have the tip4p.itp file
if i just wanted polarisable force field so as  you told me i have the 
tip4p.itp file.should i modify this file or the force field.itp file


A non-polarisable water and a polarisable rest of the force field sounds 
like an expensive random number generator. I think you need to make sure 
you're trying to do something that is backed by some peer-reviewed 
literature.


Mark



reagrds,
shree
On Mon, Dec 20, 2010 at 9:33 AM, Justin A. Lemkul > wrote:




sreelakshmi ramesh wrote:

Dear justin ,
  I read the manual and i didnt get it thats
why i sought the help of people here.i want to know how to use
those polarisable force field.


Then what you should have found is that there are no polarizable
force fields in Gromacs, but it may be possible to implement one
using the contents of sw.itp (a simple water model) as a template.
 The files you would need to create (and their contents) will be
described in Chapters 4 and 5 of the manual.  Beyond that, you
would have to be very specific as to the part(s) of implementation
with which you're having difficulty.  Otherwise, you'll just get
pointed to the manual.

-Justin

On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   sreelakshmi ramesh wrote:

   Dear all,
  can anyone tell me if there  are polarisable
force
   field available in gromacs.I need to use dang chang
force field
   which is polarisable force field for my work.I have used
   classical force fields before can anyone help me out
regaring this.


   Start by reading the manual.  All of the force fields
included in
   Gromacs are described.  Polarizability is discussed in
section 4.4,
   mostly in relation to water models.

   -Justin


   thanks in advance ,
   shree


   -- 

   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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-- 



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] Reg: fatal error pdb2gmx

[Mark Abraham]

On 20/12/2010 4:25 PM, vinothkumar mohanakrishnan wrote:

Hi all

I want to use pdb2gmx to generate hexane topology and hexane.gro file. 
i have added the atom name in .atp file and corresponding section in 
.rtp file. i have given below my .rtp entry


You don't need to add an .rtp entry, it's as much work as writing your 
molecule's .itp file and more fiddly.




[ DRG ]
 [ atoms ]
CAA opls_966   0  1
CAF opls_966   0  1
CAB opls_967   0  2
CAC opls_967   0  2
CAD opls_967   0  2
CAE opls_967   0  2

 [ bonds ]
CAACAB
CABCAC
CACCAD
CADCAE
CAECAF

 [ angles ]
CAACABCAC
CABCACCAD
CACCADCAE
CADCAECAF

 [ dihedrals ]
CAACABCACCAD
CABCACCADCAE
CACCADCAECAF

but i get the error message as given below and it doesn't generate any 
.top and .gro file . I searched the mailing list and found a similar 
post but there is no solution 
(http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) 
previously i used pdb2gmx for other molecules and it worked fine for 
the oplsaa force field. any help is highly appreciated.


Opening library file ffoplsaa.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading hexane.pdb...
Read 6 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms

  chain  #res #atoms
  1 ' ' 1  6

All occupancies are one
Opening library file ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

---
Program pdb2gmx, VERSION 4.0.7
Source code file: resall.c, line: 279

Fatal error:
in .rtp file at line:


---


Probably you've mangled the file somehow, like editing on a non-unix 
system and not changing the line endings, or transferred zero bytes of 
the file.


PRODRG will be worthless for generating parameters for any force field 
other than that which it targets. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization for 
general advice. I'd suggest throwing away what you've been trying to do, 
and seeking a force field that already has hexane-suitable parameters, 
preferably with someone else having already published using those 
parameters. If your literature search comes up empty, perhaps you should 
choose your force field according to the availability of useful 
parameterization tools (see 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation), 
rather than inventing some Frankenstein approach that your reviewer is 
likely to just laugh at.


Mark
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[gmx-users] how to add a electric field to the water box when do a simulation

[松啸天]

dear:
   I would like to use the  electric field inside a box defined by gromacs. So 
I  added E_x 1 10 0 in the .mdp file, is it  the right approach? i  hope people 
who knows will help me to add the electric field when i do a simulation.that's 
all.thank you!
 
 yours
   sincerely
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[gmx-users] search for help

[松啸天]

dear:
   I would like to use the  electric field inside a box defined by gromacs. So 
I  added E_x 1 10 0 in the .mdp file, is it  the right approach? i  hope people 
who knows will help me to add the electric field when i do a simulation.that's 
all.thank you!
 
 yours
   sincerely
  -- 
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[gmx-users] Reg: Dihedral conversion from fourier to RB form

[vinothkumar mohanakrishnan]

Hi all

I want to convert the fourier co-efficients into RB form.i have V1, V2 and
V3 in the literature. My question is V1,V2 and V3 corresponds to F1,F2 and
F3 in the manual?. I just want to confirm one more thing to convert fourier
coefficients to RB form the formula i have to use is 4.64 in the manual?i am
bit confused about the conversion. any help is highly appreciated.

Regards
Vinoth
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Re: [gmx-users] how to add a electric field to the water box when do a simulation

[Carsten Kutzner]

On Dec 20, 2010, at 12:09 PM, 松啸天 wrote:

> dear:
>I would like to use the  electric field inside a box defined by gromacs. 
> So I  added E_x 1 10 0in the .mdp file, is it  the right approach?
Yes, this will add an electric field of strength 10 V/nm acting in x-direction.

Carsten
>  i  hope people who knows will help me to add the electric field when i do a 
> simulation.that's all.thank you!
>  
>  yours
>sincerely
> -- 
> 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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Re: [gmx-users] how to add a electric field to the water box when do a simulation

[Daniel P. Luis J.]

I think you would to try 1 10.0 0.0. In the numbers,

On Mon Dec 20th, 2010 3:59 AM PST Carsten Kutzner wrote:

>On Dec 20, 2010, at 12:09 PM, 松啸天 wrote:
>
>> dear:
>>I would like to use the  electric field inside a box defined by gromacs. 
>> So I  added E_x 1 10 0in the .mdp file, is it  the right approach?
>Yes, this will add an electric field of strength 10 V/nm acting in x-direction.
>
>Carsten
>>  i  hope people who knows will help me to add the electric field when i do a 
>> simulation.that's all.thank you!
>>  
>>  yours
>>sincerely
>> -- 
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>
>--
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[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC

[Chris Neale]

Dear Gromacs users:

I pulled the master version of the source code today at 2pm via:
git clone git://git.gromacs.org/gromacs.git
and I tried to compile it following the instructions posted here: 
http://www.gromacs.org/Developer_Zone/Cmake but I was unsuccessful.  
This is my first attempt at using cmake, but I have been compiling 
gromacs successfully with autoconf since version 3.3.1


I have a recent enough version of cmake:
$ cmake --version
cmake version 2.8.0

And I have installed fftw:
$ echo $FFTW_LOCATION
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec
$ ls $FFTW_LOCATION/lib
libfftw3f.a  libfftw3f.la  libfftw3f_threads.a  libfftw3f_threads.la  
pkgconfig


But then when I try to compile gromacs:
$ cmake ../ -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include 
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a 
-DCMAKE_INSTALL_PREFIX=$(pwd) -DGMX_X11=OFF 
-DCMAKE_CXX_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc -DCMAKE_C_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc

$ make -j 4

I get the error:
...  ...
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
Linking C shared library libmd.so
ld: 
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a(mapflags.o): 
relocation R_X86_64_32S against `a local symbol' can not be used when 
making a shared object; recompile with -fPIC
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a: 
could not read symbols: Bad value

make[2]: *** [src/mdlib/libmd.so.6] Error 1
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
make: *** [all] Error 2

Just to be sure, I recompiled my FFTW and also tried a few different 
options for FFTW3F_LIBRARIES, all with errors.
This fftw was compiled the same way I did previously, but just in case 
our version of icc was updated and this is causing the problem:

export CC=icc
export CXX=icpc
./configure --enable-float --enable-threads --prefix=$(pwd)/exec
make
make install

 USING 
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a

...  ...
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'

...  ...

 78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
Linking C executable g_luck
Scanning dependencies of target g_protonate
[ 79%] Building C object 
src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
[ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so: 
warning: warning: feupdateenv is not implemented and will always fail

Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'

...  ...

Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
[ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
[ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
Linking C shared library libgmxana.so
[ 89%] Built target gmxana
make: *** [all] Error 2

 USING 
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.la

...  ...
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
Linking C shared library libmd.so
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.la: 
file not recognized: File format not recognized


 USING 
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.la

...  ...
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
Linking C shared library libmd.so
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f_threads.la: 
file not recognized: File format not recognized

make[2]: *** [src/mdlib/libmd.so.6] Error 1
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
make: *** [all] Error 2


Thank you,
Chris.
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Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC

[Roland Schulz]

You want to compile fftw with either --enable-shared or with --with-pic. Or
you need to compile a static version of Gromacs. As the message says you
can't use fftw without pic with shared libraries in GROMACS.

Roland

On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale wrote:

> Dear Gromacs users:
>
> I pulled the master version of the source code today at 2pm via:
> git clone git://git.gromacs.org/gromacs.git
> and I tried to compile it following the instructions posted here:
> http://www.gromacs.org/Developer_Zone/Cmake but I was unsuccessful.  This
> is my first attempt at using cmake, but I have been compiling gromacs
> successfully with autoconf since version 3.3.1
>
> I have a recent enough version of cmake:
> $ cmake --version
> cmake version 2.8.0
>
> And I have installed fftw:
> $ echo $FFTW_LOCATION
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec
> $ ls $FFTW_LOCATION/lib
> libfftw3f.a  libfftw3f.la  libfftw3f_threads.a  libfftw3f_threads.la pkgconfig
>
> But then when I try to compile gromacs:
> $ cmake ../ -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include
> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a
> -DCMAKE_INSTALL_PREFIX=$(pwd) -DGMX_X11=OFF
> -DCMAKE_CXX_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc
> -DCMAKE_C_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc
> $ make -j 4
>
> I get the error:
> ...  ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> ld:
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a(mapflags.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when making
> a shared object; recompile with -fPIC
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a:
> could not read symbols: Bad value
> make[2]: *** [src/mdlib/libmd.so.6] Error 1
> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
> make: *** [all] Error 2
>
> Just to be sure, I recompiled my FFTW and also tried a few different
> options for FFTW3F_LIBRARIES, all with errors.
> This fftw was compiled the same way I did previously, but just in case our
> version of icc was updated and this is causing the problem:
> export CC=icc
> export CXX=icpc
> ./configure --enable-float --enable-threads --prefix=$(pwd)/exec
> make
> make install
>
>  USING
> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a
> ...  ...
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'
>
> ...  ...
>
>  78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
> Linking C executable g_luck
> Scanning dependencies of target g_protonate
> [ 79%] Building C object
> src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
> [ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so: warning:
> warning: feupdateenv is not implemented and will always fail
> Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'
>
> ...  ...
>
> Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
> [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
> [ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
> Linking C shared library libgmxana.so
> [ 89%] Built target gmxana
> make: *** [all] Error 2
>
>  USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
> libfftw3f.la
> ...  ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.la:
> file not recognized: File format not recognized
>
>  USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
> libfftw3f_threads.la
> ...  ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
> libfftw3f_threads.la: file not recognized: File format not recognized
> make[2]: *** [src/mdlib/libmd.so.6] Error 1
> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
> make: *** [all] Error 2
>
>
> Thank you,
> Chris.
> --
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Re: [gmx-users] how to add a electric field to the water box when do a simulation

[Mark Abraham]

On 21/12/2010 3:39 AM, Daniel P. Luis J. wrote:

I think you would to try 1 10.0 0.0. In the numbers,


GROMACS does not determine whether to store an input number as an 
integer or a float based on the presence of numbers after a decimal 
point. The range of permissible values determines the data type in which 
it is stored.


Mark


On Mon Dec 20th, 2010 3:59 AM PST Carsten Kutzner wrote:


On Dec 20, 2010, at 12:09 PM, 松啸天 wrote:


dear:
I would like to use the  electric field inside a box defined by gromacs. So 
I  added E_x 1 10 0in the .mdp file, is it  the right approach?

Yes, this will add an electric field of strength 10 V/nm acting in x-direction.

Carsten

  i  hope people who knows will help me to add the electric field when i do a 
simulation.that's all.thank you!

  yours
sincerely
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[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;

[chris . neale]

 ...

 78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
Linking C executable g_luck
Scanning dependencies of target g_protonate
[ 79%] Building C object
src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
[ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so: warning:
warning: feupdateenv is not implemented and will always fail
Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'

...  ...

Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
[ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
[ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
Linking C shared library libgmxana.so
[ 89%] Built target gmxana
make: *** [all] Error 2

 USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
libfftw3f.la
...  ...
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
Linking C shared library libmd.so
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.la:
file not recognized: File format not recognized

 USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
libfftw3f_threads.la
...  ...
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
Linking C shared library libmd.so
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
libfftw3f_threads.la: file not recognized: File format not recognized
make[2]: *** [src/mdlib/libmd.so.6] Error 1
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
make: *** [all] Error 2


Thank you,
Chris.
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Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;

[Roland Schulz]

: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> Just to be sure, I recompiled my FFTW and also tried a few different
>>> options for FFTW3F_LIBRARIES, all with errors.
>>> This fftw was compiled the same way I did previously, but just in case
>>> our
>>> version of icc was updated and this is causing the problem:
>>> export CC=icc
>>> export CXX=icpc
>>> ./configure --enable-float --enable-threads --prefix=$(pwd)/exec
>>> make
>>> make install
>>>
>>>  USING
>>> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a
>>> ...  ...
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'
>>>
>>> ...  ...
>>>
>>>  78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
>>> Linking C executable g_luck
>>> Scanning dependencies of target g_protonate
>>> [ 79%] Building C object
>>> src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
>>> [ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so:
>>> warning:
>>> warning: feupdateenv is not implemented and will always fail
>>> Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'
>>>
>>> ...  ...
>>>
>>> Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
>>> [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
>>> [ 89%] Building C object
>>> src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
>>> Linking C shared library libgmxana.so
>>> [ 89%] Built target gmxana
>>> make: *** [all] Error 2
>>>
>>>  USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
>>> libfftw3f.la
>>> ...  ...
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
>>> Linking C shared library libmd.so
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
>>> libfftw3f.la:
>>> file not recognized: File format not recognized
>>>
>>>  USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
>>> libfftw3f_threads.la
>>> ...  ...
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
>>> Linking C shared library libmd.so
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
>>> libfftw3f_threads.la: file not recognized: File format not recognized
>>> make[2]: *** [src/mdlib/libmd.so.6] Error 1
>>> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>>
>>> Thank you,
>>> Chris.
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
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>> End of gmx-users Digest, Vol 80, Issue 135
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[gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

[chris . neale]

<"cmake --> relocation R_X86_64_32S against `a local symbol' can not be  
used when making a shared object;>>


Dear Roland:

It is not my intention to be confrontational, your assistance was very  
useful, I appreciate it very much, and I realize that it's not your  
job to comment everything (or even answer my questions on this mailing  
list). Further, I have actually contributed significantly to the  
gromacs wiki in the past, but it's not a wiki anymore and the barrier  
to posting is enough that I'm not the only person who has given up on  
it.


Second, I would like to mention that as a user I am extremely hesitant  
to upgrade my gromacs version due to the lack of commenting and lack  
of a good test suite. Anybody who used the free energy code with TIP4P  
in 2008/2009 or used the pull code in the early versions of gromacs 4  
will probably agree with me that testing and documentation are at  
least as important as new code.


I'm not asking anybody else to add documentation or test suites. I'm  
simply pointing out that gromacs is falling behind in these areas and  
it is not necessarily a good thing. I think that there is a utility in  
simply noting this.


Sincerely,
Chris.



-- original message --

Please contribute you experience to the wiki pages. Good documentation  
requires many people to help. The (main) developers are often too busy  
too

write detailed documentation.



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[gmx-users] Question regarding g_rdf

[rainy...@yahoo.com]

Hello,

I am fairly new to using Gromacs and am writing to seek clarification on the
g_rdf module.

In the manual, it states that "g_rdf calculates radial distribution
functions in different ways. The normal method is around a (set of)
particle(s), the other method is around the center of mass of a set of
particles."

Suppose a protein is solvated in a cubic water box.  If I interpret this
correctly, the former method only produces RDF values at a distance *outside
* of (or around) the protein.  The latter method produces RDF values within
the protein (distance from its center-of-mass).

I ask this because I am unsure how to utilize the -com flag:

$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o
rdf_protein.xvg  (first method?)

$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o
rdf_protein.xvg -com  (second method?)

Any helpful insights are most welcome.

Regards,
Lily
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Re: [gmx-users] Question regarding g_rdf

[Justin A. Lemkul]

rainy...@yahoo.com wrote:

Hello,

I am fairly new to using Gromacs and am writing to seek clarification on 
the g_rdf module.


In the manual, it states that "g_rdf calculates radial distribution 
functions in different ways. The normal method is around a (set of) 
particle(s), the other method is around the center of mass of a set of 
particles."


Suppose a protein is solvated in a cubic water box.  If I interpret this 
correctly, the former method only produces RDF values at a distance 
/outside/ of (or around) the protein.  The latter method produces RDF 
values within the protein (distance from its center-of-mass).




Your interpretation is incorrect.  A normal RDF plots probabilities of distances 
between any atom pairs in the given index groups.  Invoking the -com flag simply 
means that the center of mass of the protein, not all of its constituent atoms 
individually, is used as the reference in the RDF plot.


-Justin


I ask this because I am unsure how to utilize the -com flag:

$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o 
rdf_protein.xvg  (first method?)


$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o 
rdf_protein.xvg -com  (second method?)


Any helpful insights are most welcome.

Regards,
Lily



--


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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] compilation instructions, the gromacs wiki, documentation, and test suites

[Roland Schulz]

Chris,

sorry I didn't pay attention (was in a hurry). I know that you have helped
with the documentation and wouldn't have suggested to you to put it on the
wiki if I recognized it was you. I thought it was a new user. And I didn't
want to criticize but only point out (to the assumed new user) that the wiki
can be improved by everyone.

Do you have suggestion of how to improve the documentation or the test
suite? What is the barrier to the wiki?
I have mentioned that before (on the dev-list) but I think a monthly phone
conference could help to coordinate those kind of issues.

Roland

On Mon, Dec 20, 2010 at 10:07 PM,  wrote:

> < "cmake --> relocation R_X86_64_32S against `a local symbol' can not be used
> when making a shared object;>>
>
> Dear Roland:
>
> It is not my intention to be confrontational, your assistance was very
> useful, I appreciate it very much, and I realize that it's not your job to
> comment everything (or even answer my questions on this mailing list).
> Further, I have actually contributed significantly to the gromacs wiki in
> the past, but it's not a wiki anymore and the barrier to posting is enough
> that I'm not the only person who has given up on it.
>
> Second, I would like to mention that as a user I am extremely hesitant to
> upgrade my gromacs version due to the lack of commenting and lack of a good
> test suite. Anybody who used the free energy code with TIP4P in 2008/2009 or
> used the pull code in the early versions of gromacs 4 will probably agree
> with me that testing and documentation are at least as important as new
> code.
>
> I'm not asking anybody else to add documentation or test suites. I'm simply
> pointing out that gromacs is falling behind in these areas and it is not
> necessarily a good thing. I think that there is a utility in simply noting
> this.
>
> Sincerely,
> Chris.
>
>
>
> -- original message --
>
> Please contribute you experience to the wiki pages. Good documentation
> requires many people to help. The (main) developers are often too busy too
> write detailed documentation.
>
>
>
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[gmx-users] reagrding huggins meyer potential

[sreelakshmi ramesh]

Dear all,
 I wanted to simulate Nacl in water using huggins meyer
potential as vdw type.since gromacs has just LJ OR BJ potential i wanted to
know if somebody had done it with huggins meyer potential.I read the manual
and since i am not good in c or fortran i dono how to create  a user defined
potential as well.can anybody help me out with this issue.
thanks in advance.
sree.
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