[gmx-users] Reg Mpi run Error

2013-08-31 Thread vidhya sankar
Dear Jutin and Marks  Thnak you for your previous  reply
Whrn i run the following job in cluster  as follows

[hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile 
~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v -deffnm 
CNTPEPRSOLIONSfull -cpt 2

I have eceived the error as follows
Sisters Have Always Fascinated Me" (Speech)
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 3 out of 8
Halting parallel program mdrun_mpi on CPU 4 out of 8
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_6]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
[cli_2]:
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_5]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_4]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 65280
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES


what is the meaning of above error  How to solve it?

Thanks in advance

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Re: [gmx-users] Reg Mpi run Error

2013-08-31 Thread Justin Lemkul



On 8/31/13 4:54 AM, vidhya sankar wrote:

Dear Jutin and Marks  Thnak you for your previous  reply
Whrn i run the following job in cluster  as follows

[hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile 
~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v -deffnm 
CNTPEPRSOLIONSfull -cpt 2

I have eceived the error as follows
Sisters Have Always Fascinated Me" (Speech)
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 3 out of 8
Halting parallel program mdrun_mpi on CPU 4 out of 8
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_6]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
[cli_2]:
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_5]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
gcq#33: "Sisters Have Always Fascinated Me" (Speech)
[cli_4]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 65280
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES


what is the meaning of above error  How to solve it?



These are generic mpirun failure messages.  The real error is further up in the 
screen output or in the .log file.


-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] Reg mpirun error

2013-08-31 Thread vidhya sankar
Thank you justin for your reply

The error I have pasted here (also pasted in previous mail)
is total screen ouptut. No further output as you stated in previous mail( The 
real error is further up in the 
screen output or in the .log file.) 



>
 [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 
-machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v 
-deffnm CNTPEPRSOLIONSfull -cpt 2
>
> I have eceived the error as follows
> Sisters Have Always Fascinated Me" (Speech)
> Error on node 3, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 3 out of 8
> Halting parallel program mdrun_mpi on CPU 4 out of 8
> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
> [cli_6]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
> [cli_3]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
> [cli_2]:
> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
> [cli_5]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
> aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
> [cli_4]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
>
> ===
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 65280
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
 you Mailed me this is generic mpirun  error (These are generic mpirun failure 
messages)  But No error message shown in .log file


Could you please help to solve this error?

With Regards
S.Vidhyasankar
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Re: [gmx-users] Reg mpirun error

2013-08-31 Thread Mark Abraham
Run it again, this time re-directing stderr and stdout to files so
that you can read them later. (Google for how to do that with your
shell.)

Mark

On Sat, Aug 31, 2013 at 1:47 PM, vidhya sankar  wrote:
> Thank you justin for your reply
>
> The error I have pasted here (also pasted in previous mail)
> is total screen ouptut. No further output as you stated in previous mail( The 
> real error is further up in the
> screen output or in the .log file.)
>
>
>
>>
>  [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8
> -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v
> -deffnm CNTPEPRSOLIONSfull -cpt 2
>>
>> I have eceived the error as follows
>> Sisters Have Always Fascinated Me" (Speech)
>> Error on node 3, will try to stop all the nodes
>> Halting parallel program mdrun_mpi on CPU 3 out of 8
>> Halting parallel program mdrun_mpi on CPU 4 out of 8
>> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
>> [cli_6]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
>> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
>> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
>> [cli_3]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
>> [cli_2]:
>> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
>> [cli_5]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
>> aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
>> gcq#33: "Sisters Have Always Fascinated Me" (Speech)
>> [cli_4]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
>>
>> ===
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   EXIT CODE: 65280
>> =   CLEANING UP REMAINING PROCESSES
>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>
>  you Mailed me this is generic mpirun  error (These are generic mpirun 
> failure messages)  But No error message shown in .log file
>
>
> Could you please help to solve this error?
>
> With Regards
> S.Vidhyasankar
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[gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi

Hi!

I am currently using "mdrun -rerun" in order to get the energy of a system 
to be used in a Monte Carlo algortihm. A while ago, I was pointed to 
Grompy which should be capable of performing Monte Carlo using gromacs 
libraries (my description might not be very accurate here). I have 
downloaded grompy from git but I cannot find my way through (sorry, I'm 
rusty with python).


Is there a way how I can directly call the gromacs energy routine from 
python and/or TCL? "mdrun -rerun" works but it creates overhead because 
the conformation has to be written to disk, then read by mdrun which 
writes an energy file that needs to be read by g_energy. I would like to 
have a library that can be called from my TCL/python script.


I would appreciate any help on this.

Thanks,

 Gianluca

PS: According to the roadmap MC should be available in version 5.0 but 
until it's released I need to find an alternative :)


-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi
After reading a bit more in the grompy directory, I found that the file 
__init__.py loads the necessary libraries, e.g., mdrun.so. This is because 
gromacs (they use version 4.0.7) was compiled with the flag 
--enable-shared. I am using version 4.6.3 which uses "cmake" instead of 
"configure". Is there an equivalent flag for cmake that corresponds to 
"--enable-shared"?


Thanks,

 Gianluca

On Sat, 31 Aug 2013, Gianluca Interlandi wrote:


Hi!

I am currently using "mdrun -rerun" in order to get the energy of a system to 
be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy 
which should be capable of performing Monte Carlo using gromacs libraries (my 
description might not be very accurate here). I have downloaded grompy from 
git but I cannot find my way through (sorry, I'm rusty with python).


Is there a way how I can directly call the gromacs energy routine from python 
and/or TCL? "mdrun -rerun" works but it creates overhead because the 
conformation has to be written to disk, then read by mdrun which writes an 
energy file that needs to be read by g_energy. I would like to have a library 
that can be called from my TCL/python script.


I would appreciate any help on this.

Thanks,

Gianluca

PS: According to the roadmap MC should be available in version 5.0 but until 
it's released I need to find an alternative :)


-
Gianluca Interlandi, PhD gianl...@u.washington.edu
   +1 (206) 685 4435
   http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
   http://healthynaturalbaby.org
-
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Justin Lemkul



On 8/31/13 2:16 PM, Gianluca Interlandi wrote:

After reading a bit more in the grompy directory, I found that the file
__init__.py loads the necessary libraries, e.g., mdrun.so. This is because
gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I
am using version 4.6.3 which uses "cmake" instead of "configure". Is there an
equivalent flag for cmake that corresponds to "--enable-shared"?



-DBUILD_SHARED_LIBS=ON

-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] question about g_hydorder

2013-08-31 Thread Nidhi Katyal
Dear all
I would like to calculate angle tetrahedral order parameter of water
molecules as defined by  Chau et al (eq 3). I am using g_hydorder of
gromacs 4.6.3 with my index group containing all oxygen atoms of water:
g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
file_2.out -n index.ndx
I am getting following error;
No or not correct number (2) of output files :1
It seems from above that correct number should be 2 but user is supplying
only 1 and so is the error. But I am giving names of two output files.
Also, I am unable to understand what exactly is contained in these two/four
output files. I tried to comprehend this by looking at gmx_hydorder.c and
could make a guess that I actually need sgmol/sgmean (variables as defined
in program) as the final output.
Please help me understand the usage of this command in order to fulfill my
aim.Thanks in advance.
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi

Thanks Justin.

I have been wondering where I can find all options of cmake (./configure 
--help used to print all possible options, whereas cmake --help prints out 
just the usage of cmake itself).


Gianluca

On Sat, 31 Aug 2013, Justin Lemkul wrote:




On 8/31/13 2:16 PM, Gianluca Interlandi wrote:

After reading a bit more in the grompy directory, I found that the file
__init__.py loads the necessary libraries, e.g., mdrun.so. This is because
gromacs (they use version 4.0.7) was compiled with the flag 
--enable-shared. I
am using version 4.6.3 which uses "cmake" instead of "configure". Is there 
an

equivalent flag for cmake that corresponds to "--enable-shared"?



-DBUILD_SHARED_LIBS=ON

-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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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Justin Lemkul



On 8/31/13 2:32 PM, Gianluca Interlandi wrote:

Thanks Justin.

I have been wondering where I can find all options of cmake (./configure --help
used to print all possible options, whereas cmake --help prints out just the
usage of cmake itself).



There's nothing like this that I'm aware of, but that's a problem on the CMake 
level, not the Gromacs level.  There are lots of threads online asking the same 
thing.  There are several methods for going through the CMake options, including 
interactively and/or via a GUI.  See 
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/Cmake.


-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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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi
I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries 
that I find are:


libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is 
no library called libmdrun.so like the one used in grompy. Could it be 
that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the 
command mdrun call libmd.so?


Thanks,

 Gianluca

On Sat, 31 Aug 2013, Justin Lemkul wrote:




On 8/31/13 2:16 PM, Gianluca Interlandi wrote:

After reading a bit more in the grompy directory, I found that the file
__init__.py loads the necessary libraries, e.g., mdrun.so. This is because
gromacs (they use version 4.0.7) was compiled with the flag 
--enable-shared. I
am using version 4.6.3 which uses "cmake" instead of "configure". Is there 
an

equivalent flag for cmake that corresponds to "--enable-shared"?



-DBUILD_SHARED_LIBS=ON

-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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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Justin Lemkul



On 8/31/13 3:04 PM, Gianluca Interlandi wrote:

I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I
find are:

libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no
library called libmdrun.so like the one used in grompy. Could it be that
libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun
call libmd.so?



I have never heard of anything called "libmdrun.so" and I do not see one in any 
of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command should 
be linked against libmd.so; you can check with ldd.


-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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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Justin Lemkul



On 8/31/13 3:11 PM, Justin Lemkul wrote:



On 8/31/13 3:04 PM, Gianluca Interlandi wrote:

I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I
find are:

libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no
library called libmdrun.so like the one used in grompy. Could it be that
libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun
call libmd.so?



I have never heard of anything called "libmdrun.so" and I do not see one in any
of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command should
be linked against libmd.so; you can check with ldd.



A quick look through the GromPy documentation suggests that libmdrun.so is 
something that GromPy creates through one of its scripts.  Having never used 
GromPy, that's the best I can offer.


-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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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi
Thanks for looking into that. I wonder whether routines of libmd.so can be 
called directly from a python script just like grompy calles routines from 
libmdrun.so


I wonder if I can find more documentation about this topic.

There is a python wrapper for gromacs functions here:

http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/

and a thread in the developers discussion:

http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html

Gianluca

On Sat, 31 Aug 2013, Justin Lemkul wrote:




On 8/31/13 3:11 PM, Justin Lemkul wrote:



On 8/31/13 3:04 PM, Gianluca Interlandi wrote:
I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries 
that I

find are:

libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is 
no

library called libmdrun.so like the one used in grompy. Could it be that
libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command 
mdrun

call libmd.so?



I have never heard of anything called "libmdrun.so" and I do not see one in 
any
of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command 
should

be linked against libmd.so; you can check with ldd.



A quick look through the GromPy documentation suggests that libmdrun.so is 
something that GromPy creates through one of its scripts.  Having never used 
GromPy, that's the best I can offer.


-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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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Mark Abraham
On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi
 wrote:
> Thanks for looking into that. I wonder whether routines of libmd.so can be
> called directly from a python script just like grompy calles routines from
> libmdrun.so

One could do so, but the GROMACS "libraries" are not built with this
kind of usage in mind, and (for example) will issue a fatal error
whenever that seems right. This will also kill the calling program,
which is usually unacceptable. There's a current thread on gmx-users
asking about library-type functionality, too. Better behaviour isn't
likely to happen until someone steps up to make the code changes. So
far it's not a priority for anyone who knows the code well enough to
do it, and the learning curve too daunting for everyone else! :-)

One doesn't have to hit disk with output files, either. Memory-mapped
files and named pipes can be useful.

Mark

> I wonder if I can find more documentation about this topic.
>
> There is a python wrapper for gromacs functions here:
>
> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/
>
> and a thread in the developers discussion:
>
> http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html
>
> Gianluca
>
>
> On Sat, 31 Aug 2013, Justin Lemkul wrote:
>
>>
>>
>> On 8/31/13 3:11 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 8/31/13 3:04 PM, Gianluca Interlandi wrote:

 I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries
 that I
 find are:

 libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

 which are also produced without specifying -DBUILD_SHARED_LIBS=ON There
 is no
 library called libmdrun.so like the one used in grompy. Could it be that
 libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command
 mdrun
 call libmd.so?

>>>
>>> I have never heard of anything called "libmdrun.so" and I do not see one
>>> in any
>>> of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command
>>> should
>>> be linked against libmd.so; you can check with ldd.
>>>
>>
>> A quick look through the GromPy documentation suggests that libmdrun.so is
>> something that GromPy creates through one of its scripts.  Having never used
>> GromPy, that's the best I can offer.
>>
>> -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
>>
>> ==
>> --
>> 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
>>
>
> -
> Gianluca Interlandi, PhD gianl...@u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> http://healthynaturalbaby.org
> -
> --
> 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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> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] grompy and how to call energy routine

2013-08-31 Thread Gianluca Interlandi

Dear Mark,

Thank you very much for the enlightment. I will look into named pipes. 
This might be appropriate since I'm calling mdrun from a TCL script in 
VMD.


Gianluca

On Sun, 1 Sep 2013, Mark Abraham wrote:


On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi
 wrote:

Thanks for looking into that. I wonder whether routines of libmd.so can be
called directly from a python script just like grompy calles routines from
libmdrun.so


One could do so, but the GROMACS "libraries" are not built with this
kind of usage in mind, and (for example) will issue a fatal error
whenever that seems right. This will also kill the calling program,
which is usually unacceptable. There's a current thread on gmx-users
asking about library-type functionality, too. Better behaviour isn't
likely to happen until someone steps up to make the code changes. So
far it's not a priority for anyone who knows the code well enough to
do it, and the learning curve too daunting for everyone else! :-)

One doesn't have to hit disk with output files, either. Memory-mapped
files and named pipes can be useful.

Mark


I wonder if I can find more documentation about this topic.

There is a python wrapper for gromacs functions here:

http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/

and a thread in the developers discussion:

http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html

Gianluca


On Sat, 31 Aug 2013, Justin Lemkul wrote:




On 8/31/13 3:11 PM, Justin Lemkul wrote:




On 8/31/13 3:04 PM, Gianluca Interlandi wrote:


I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries
that I
find are:

libmd.so libgmxana.so libgmxpreprocess.so libgmx.so

which are also produced without specifying -DBUILD_SHARED_LIBS=ON There
is no
library called libmdrun.so like the one used in grompy. Could it be that
libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command
mdrun
call libmd.so?



I have never heard of anything called "libmdrun.so" and I do not see one
in any
of my current installations - 4.0.7, 4.5.5, or 4.6.3.  The mdrun command
should
be linked against libmd.so; you can check with ldd.



A quick look through the GromPy documentation suggests that libmdrun.so is
something that GromPy creates through one of its scripts.  Having never used
GromPy, that's the best I can offer.

-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

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
--
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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ww

[gmx-users] Umbrella Sampling PMF

2013-08-31 Thread Shima Arasteh
Hi,


I ran US on an ion through a channel inserted in a bilayer.

I used g_wham and got the profile output. In the visualized profile, I see a 
region that the plot shows a flat line and it seems the data is missed there. 
Would you please let me know what the reason of missing data is?



Thanks for your suggestions in advance.

 
Sincerely,
Shima
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