date:20130607

Dear Gmx Users,

I want to specify a table to mdrun for non bonded parameters. I wish to set
it up for all atoms with same potential. Is there any example of the table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?

Thanks

Steven
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[gmx-users] Problems building gromacs 4.6

2013-06-07 Thread colinbannister

I am trying to build Gromacs 4.6 on a Linux machine, running Scientific Linux
6.2.  I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.

Commands I issue to set environment, and run cmake (available as cmake28)
are:

[cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler/64
[cczcb@login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0
[cczcb@login02 gromacs-build-nocuda]$ module load intel/mkl/64  
[cczcb@login02 gromacs-build-nocuda]$ export CC=mpicc
[cczcb@login02 gromacs-build-nocuda]$ export CXX=mpicxx
[cczcb@login02 gromacs-build-nocuda]$ mklvars_intel64.sh
[cczcb@login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6
-DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON
-DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/include
-DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so

This completes, but gives Segmentation fault messages at the end.  Output
attached as 'cmake28.out'

When I type 'make', it gets to 53% then gives a large number of 'undefined
reference' errors, see 'make.out'.

I have also tried only putting the libmkl_core.so library path as the
setting for MKL_LIBRARIES.  This avoids the Segmentation faults, but again
results in many undefined references, as you might expect.

Any idea what could be happening here ?  Is Cmake messing up in parsing the
command in some way ?  Is there a different approach I could use to build
Gromacs ?

Any assistance much appreciated!

Colin

cmake28.out http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out  
make.out http://gromacs.5086.x6.nabble.com/file/n5008889/make.out  




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Re: [gmx-users] User-define non bonded table

2013-06-07 Thread Mohan maruthi sena

 Hi Neumann,
You  can use tabulated potential option in
gromacs. Please check the site given below:
 http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Thanks,
Mohan


On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Dear Gmx Users,

 I want to specify a table to mdrun for non bonded parameters. I wish to set
 it up for all atoms with same potential. Is there any example of the table
 like this? I want use my specific potential so table should have two
 columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
 How can I tell gromacs to use it for all interactions?

 Thanks

 Steven
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Re: [gmx-users] User-define non bonded table

Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?

Steven


On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:

  Hi Neumann,
 You  can use tabulated potential option in
 gromacs. Please check the site given below:
  http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

 Thanks,
 Mohan


 On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
 wrote:

  Dear Gmx Users,
 
  I want to specify a table to mdrun for non bonded parameters. I wish to
 set
  it up for all atoms with same potential. Is there any example of the
 table
  like this? I want use my specific potential so table should have two
  columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
  How can I tell gromacs to use it for all interactions?
 
  Thanks
 
  Steven
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[gmx-users] Re: using previous window restart file

2013-06-07 Thread gromacs query

Dear All,

Please any suggestion?

regards,


On Mon, Jun 3, 2013 at 4:53 PM, gromacs query gromacsqu...@gmail.comwrote:

 Dear All,

 (Sorry for long mail!)

 (Thanks Thomas Schlesier for clarifying previous umbrella queries)

 I wish to run umbrella samplings using restart file of previous window.
 e.g. initial distance between A (reference) and B (pulled group) is 1 nm
 (10 Angs) then I intend to run 10 windows after each 1 Angstrom. Due to
 some reasons I want to use restart file of previous window, so if suppose
 1st window (10 Angstrom window) is done then I will use last restart file
 of 1st window for 2nd window (9 Angstrom window)

 (This is different from Justin's tutorial in which initial configurations
 are generated in single pulling experiment).

  In such case as I said I want to use last restart of 1st Window for 2nd
 window so obviously the distance will not be exactly 9 Angstrom between A
 and B for 1st window restart file. What approach I should use for adjusting
 initial distance being 9 Angstrom to get initial configuration for 2nd
 window

 Knowing the distance between A and B in the restart file of 1st window
 (say 'x')
 then for second window y = 9 - x (where x can be  or  9),


 First approach:

 pull_rate1  = (y/1000) or even slower


 Second approach:

 pull_init1  = y
 pull_rate1  = 0.0


 Please Note for both the cases I can use pull_vec1 or pull rates (- or +)
 for positive or negative relative movement to get exact 9 Angstrom window
 distance

 regards,
 Jiomm

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Re: [gmx-users] Re: using previous window restart file




On 6/7/13 7:41 AM, gromacs query wrote:

Dear All,

Please any suggestion?



I think you should be able to set whatever value you like for pull_init1 and the 
code should take care of it.


-Justin



On Mon, Jun 3, 2013 at 4:53 PM, gromacs query gromacsqu...@gmail.comwrote:


Dear All,

(Sorry for long mail!)

(Thanks Thomas Schlesier for clarifying previous umbrella queries)

I wish to run umbrella samplings using restart file of previous window.
e.g. initial distance between A (reference) and B (pulled group) is 1 nm
(10 Angs) then I intend to run 10 windows after each 1 Angstrom. Due to
some reasons I want to use restart file of previous window, so if suppose
1st window (10 Angstrom window) is done then I will use last restart file
of 1st window for 2nd window (9 Angstrom window)

(This is different from Justin's tutorial in which initial configurations
are generated in single pulling experiment).

  In such case as I said I want to use last restart of 1st Window for 2nd
window so obviously the distance will not be exactly 9 Angstrom between A
and B for 1st window restart file. What approach I should use for adjusting
initial distance being 9 Angstrom to get initial configuration for 2nd
window

Knowing the distance between A and B in the restart file of 1st window
(say 'x')
then for second window y = 9 - x (where x can be  or  9),


First approach:

pull_rate1  = (y/1000) or even slower


Second approach:

pull_init1  = y
pull_rate1  = 0.0


Please Note for both the cases I can use pull_vec1 or pull rates (- or +)
for positive or negative relative movement to get exact 9 Angstrom window
distance

regards,
Jiomm



--


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] User-define non bonded table




On 6/7/13 7:36 AM, Steven Neumann wrote:

Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?



You can start the table from whatever value of x that you like, but at a certain 
point, it is unlikely that particles ever come that close, given normal 
repulsive potentials.


-Justin


On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:


  Hi Neumann,
 You  can use tabulated potential option in
gromacs. Please check the site given below:
  http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Thanks,
Mohan


On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com

wrote:



Dear Gmx Users,

I want to specify a table to mdrun for non bonded parameters. I wish to

set

it up for all atoms with same potential. Is there any example of the

table

like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?

Thanks

Steven
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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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Re: [gmx-users] User-define non bonded table

Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :

[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

or

[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05

Or maybe both?


On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/7/13 7:36 AM, Steven Neumann wrote:

 Thank you, just getting into this. I just dont understand why they start
 from x=0.04? Why not 0.02 or sth else?


 You can start the table from whatever value of x that you like, but at a
 certain point, it is unlikely that particles ever come that close, given
 normal repulsive potentials.

 -Justin


  On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
 maruthi.s...@gmail.comwrote:

Hi Neumann,
  You  can use tabulated potential option in
 gromacs. Please check the site given below:
   
 http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

 Thanks,
 Mohan


 On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com

 wrote:


  Dear Gmx Users,

 I want to specify a table to mdrun for non bonded parameters. I wish to

 set

 it up for all atoms with same potential. Is there any example of the

 table

 like this? I want use my specific potential so table should have two
 columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
 How can I tell gromacs to use it for all interactions?

 Thanks

 Steven
 --
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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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==

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Re: [gmx-users] User-define non bonded table




On 6/7/13 8:21 AM, Steven Neumann wrote:

Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :

[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

or

[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05

Or maybe both?



Try the tutorial first and make sure you can replicate it.  If you're just 
looking to tweak C6 and C12 parameters, there's no need for tabulated functions 
at all.


-Justin



On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:




On 6/7/13 7:36 AM, Steven Neumann wrote:


Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?



You can start the table from whatever value of x that you like, but at a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.

-Justin


  On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena

maruthi.s...@gmail.comwrote:

Hi Neumann,

  You  can use tabulated potential option in
gromacs. Please check the site given below:
   
http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Thanks,
Mohan


On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com


wrote:



  Dear Gmx Users,


I want to specify a table to mdrun for non bonded parameters. I wish to


set


it up for all atoms with same potential. Is there any example of the


table


like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?

Thanks

Steven
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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/justinhttp://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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Re: [gmx-users] User-define non bonded table

On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/7/13 8:21 AM, Steven Neumann wrote:

 Thank you.
 Another question... I specify in my table functions e.g. g(x) and h(x) and
 it is written that I need to setup parameters C6 and C12. But where I
 should specify them? In :

 [ atomtypes ]
 ;name at.num mass charge ptype V(c6) W(c12)
 O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

 or

 [ nonbond_params ]
 ; i j func V(c6) W(c12)
 O O 1 0.22617E-02 0.74158E-06
 O OA 1 0.22617E-02 0.13807E-05

 Or maybe both?


 Try the tutorial first and make sure you can replicate it.  If you're just
 looking to tweak C6 and C12 parameters, there's no need for tabulated
 functions at all.

 -Justin



I want to change function g(x) to use Chandler Anderson potential so g(x) =
1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?



 On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/7/13 7:36 AM, Steven Neumann wrote:

  Thank you, just getting into this. I just dont understand why they start
 from x=0.04? Why not 0.02 or sth else?


  You can start the table from whatever value of x that you like, but at
 a
 certain point, it is unlikely that particles ever come that close, given
 normal repulsive potentials.

 -Justin


   On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena

 maruthi.s...@gmail.comwrote:

 Hi Neumann,

   You  can use tabulated potential option
 in
 gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/
 Tabulated_Potentialshttp://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials
 http://**www.gromacs.org/Documentation/**How-tos/Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
 


 Thanks,
 Mohan


 On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com

  wrote:


   Dear Gmx Users,


 I want to specify a table to mdrun for non bonded parameters. I wish
 to

  set

  it up for all atoms with same potential. Is there any example of the

  table

  like this? I want use my specific potential so table should have two
 columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
 right?
 How can I tell gromacs to use it for all interactions?

 Thanks

 Steven
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 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
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Re: [gmx-users] Is non-linear data output/storage possible?

That is all that is possible.

Mark


On Fri, Jun 7, 2013 at 4:31 AM, Dallas Warren dallas.war...@monash.eduwrote:

 Easiest, naïve way that I can see is to do the simulation in blocks, and
 change the output settings within the mdp file used as required for each
 block.

 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 Neha
  Sent: Thursday, 6 June 2013 11:00 PM
  To: gmx-users@gromacs.org
  Subject: [gmx-users] Is non-linear data output/storage possible?
 
  Hi everybody!
 
  This is a sort-of general question that I am not sure where to find the
  answer for. I am running a simulation on the order of tens of
  microseconds.
  However I also want to do some analysis on the order of very small time
  steps but I do not want to save the data of very small time steps
  throughout
  the length of the simulation as it will be taxing for the memory. I was
  wondering if there was a way to be able to store small time steps for a
  small time during the simulation and continue to increase the amount of
  time
  that energy/forces/coordinates are written and stored?
 
  I understand the mdp files control the output, but I do not know how to
  have
  a non-linear output of data using nstxout etc. Please let me know if
  you
  have any ideas/have succeeded in getting Gromacs to do this!
 
 
 
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Re: [gmx-users] User-define non bonded table

It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some values so the potential will equal zero?


On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann s.neuman...@gmail.comwrote:




 On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/7/13 8:21 AM, Steven Neumann wrote:

 Thank you.
 Another question... I specify in my table functions e.g. g(x) and h(x)
 and
 it is written that I need to setup parameters C6 and C12. But where I
 should specify them? In :

 [ atomtypes ]
 ;name at.num mass charge ptype V(c6) W(c12)
 O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

 or

 [ nonbond_params ]
 ; i j func V(c6) W(c12)
 O O 1 0.22617E-02 0.74158E-06
 O OA 1 0.22617E-02 0.13807E-05

 Or maybe both?


 Try the tutorial first and make sure you can replicate it.  If you're
 just looking to tweak C6 and C12 parameters, there's no need for tabulated
 functions at all.

 -Justin



 I want to change function g(x) to use Chandler Anderson potential so g(x)
 = 1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
 function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
 can I specify my my own C6 C12 ?



 On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/7/13 7:36 AM, Steven Neumann wrote:

  Thank you, just getting into this. I just dont understand why they
 start
 from x=0.04? Why not 0.02 or sth else?


  You can start the table from whatever value of x that you like, but
 at a
 certain point, it is unlikely that particles ever come that close, given
 normal repulsive potentials.

 -Justin


   On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena

 maruthi.s...@gmail.comwrote:

 Hi Neumann,

   You  can use tabulated potential option
 in
 gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/
 Tabulated_Potentialshttp://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials
 http://**www.gromacs.org/Documentation/**
 How-tos/Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
 


 Thanks,
 Mohan


 On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com

  wrote:


   Dear Gmx Users,


 I want to specify a table to mdrun for non bonded parameters. I wish
 to

  set

  it up for all atoms with same potential. Is there any example of the

  table

  like this? I want use my specific potential so table should have two
 columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
 right?
 How can I tell gromacs to use it for all interactions?

 Thanks

 Steven
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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/justinhttp://vt.edu/Pages/Personal/justin

Re: [gmx-users] Problems building gromacs 4.6

On Fri, Jun 7, 2013 at 12:20 PM, colinbannister
colin.bannis...@nottingham.ac.uk wrote:

I am trying to build Gromacs 4.6 on a Linux machine, running Scientific
Linux
6.2. I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.

Commands I issue to set environment, and run cmake (available as cmake28)
are:

[cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler/64
[cczcb@login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0
[cczcb@login02 gromacs-build-nocuda]$ module load intel/mkl/64
[cczcb@login02 gromacs-build-nocuda]$ export CC=mpicc
[cczcb@login02 gromacs-build-nocuda]$ export CXX=mpicxx
[cczcb@login02 gromacs-build-nocuda]$ mklvars_intel64.sh
[cczcb@login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6
-DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON
-DGMX_FFT_LIBRARY=mkl

-DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/include

-DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so

This completes, but gives Segmentation fault messages at the end. Output
attached as 'cmake28.out'

When I type 'make', it gets to 53% then gives a large number of 'undefined
reference' errors, see 'make.out'.

I have also tried only putting the libmkl_core.so library path as the
setting for MKL_LIBRARIES. This avoids the Segmentation faults, but again
results in many undefined references, as you might expect.

Any idea what could be happening here ? Is Cmake messing up in parsing the
command in some way ? Is there a different approach I could use to build
Gromacs ?

All that sounds very weird, and makes me wonder whether an MKL test program
would compile on your system. Since the value of MKL is very limited, I
would suggest compiling with FFTW for now.

GROMACS 4.6.2 streamlined the MKL build process greatly for icc = 11, but
I would suggest waiting until GROMACS 4.6.3, because of a performance
regression with MPI builds that we are working on fixing.

Cheers,

Mark

Any assistance much appreciated!

Colin

cmake28.out http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out
make.out http://gromacs.5086.x6.nabble.com/file/n5008889/make.out

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Re: [gmx-users] Unable to download Gromacs source tar file

They're fine now. Perhaps the FTP server was offline briefly.

Mark


On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy 
bhamymait...@aero.iisc.ernet.in wrote:


 Hi,
 I would like to use Gromacs for MD simulation of biomolecules. But I am
 not able to download any of the source files from the link
 http://www.gromacs.org/Downloads

 Can anyone please help.
 Thanks and regards,
 Maithry

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Re: [gmx-users] Regarding mdrun

Can't say On the information given, something about the protocol might be
too aggressive.

Mark


On Fri, Jun 7, 2013 at 7:56 AM, Venkat Reddy venkat...@gmail.com wrote:

 Dear gmx-users,
 I am experiencing some strange things while performing mdrun. I am running
 a CG simulation and it is terminating with LINCS warnings after approx.
 500ns of simulation. If I restart it with the check point file, then its
 running with out any errors. Is my simulation is reliable?? I am using
 Gromacs-4.5.5.

 Thank you

 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036
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Re: [gmx-users] Getting .edr file data as a generic data file

On Thu, Jun 6, 2013 at 5:14 PM, Neha nshafi...@wesleyan.edu wrote:

Hi again!

At the moment, the only way I know how to access .edr files is through the
use of g_energy. However g_energy only outputs .xvg files which is fine for
routine analysis. However if I want to get into further processing, it
would
be helpful if I could get the information stored in the .edr files in a
more
pliable format.

It doesn't get more pliable than the plain text in .xvg! But there are some
ideas here http://www.gromacs.org/Documentation/How-tos/Graphing_Data

Mark

Please let me know if you know how to do this! I am a completely new user to
Gromacs and appreciate all the help possible.

-Neha

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Re: [gmx-users] velocity-verlet giving nans

Don't know, but re-interpreting the old velocities at a new time might not
be fully integrated with things calculated from the old velocities, such as
temperature-coupling quantities. For switching integrators, you will need
to re-equilibrate, so you may as well generate new velocities and avoid the
problem.

If you want to suggest fixing any possible problem, please file an issue at
redmine.gromacs.org

Cheers,

Mark


On Thu, Jun 6, 2013 at 4:38 AM, Sikandar Mashayak symasha...@gmail.comwrote:

 Hi

 I first performed a simulation using leap-frog integrator, which went well
 and got the expected results. For post-processing I want velocities at full
 time step, but, as per my understanding, leap-frog computes and writes
 velocities at half-time step. Therefore, I just changed integrator from
 'md' to 'md-vv', i.e., velocity verlet. Unfortunately, after this change in
 .mdp file (i.e. keeping all other settings exactly same as previous
 leap-frog run) when I run 'mdrun' I am getting 'nan' in output from the
 first step itself.

 So I am wondering what could be the reason for this behavior of 'md-vv'
 integrator.

 Thanks
 Sikandar
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Re: [gmx-users] Case sensitivity in atomtypes

On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
bat.demou...@gmail.comwrote:

 Hello GMX users,

 I have some troubles with overriding parameters. I have generated
 parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF,
 and Acpype. This forcefield contains atomtypes cA, cB for instance. When I
 include the bonded parameters in [bondtypes], [angletypes] sections of my
 topology, or alternatively in ffbonded.itp, grompp returns warning
 concerning overriding of bonds and angles involving CA, CB, HA, ... (AMBER
 atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA, ...).

 WARNING 1 [file ffbonded.itp, line 222]:
   Overriding Bond parameters.

   old: 0.137 435136 0.137 435136 --- VALUE FOR AMBER FF FOR CB-CB
 BOND
   new: cB cB   11.3240e-014.9346e+05 --- VALUE FOR LIPID11
 cB-cB


 WARNING 2 [file ffbonded.itp, line 225]:
   Overriding Bond parameters.

   old: 0.1404 392459 0.1404 392459
   new: cA cB   11.5080e-012.7472e+05


 WARNING 3 [file ffbonded.itp, line 227]:
   Overriding Bond parameters.

   old: 0.1381 357314 0.1381 357314
   new: nA cA   11.4990e-012.4568e+05


 WARNING 4 [file ffbonded.itp, line 228]:
   Overriding Bond parameters.

   old: 0.108 307106 0.108 307106
   new: cA hA   11.0920e-012.8225e+05


 WARNING 5 [file ffbonded.itp, line 229]:
   Overriding Bond parameters.

   old: 0.14 392459 0.14 392459
   new: cA cA   11.5350e-012.5363e+05


 WARNING 6 [file ffbonded.itp, line 760]:
   Overriding Angle parameters.

   old: 120 527.184 120 527.184
   new: cA cA cA   11.1063e+025.2894e+02


 WARNING 7 [file ffbonded.itp, line 773]:
   Overriding Angle parameters.

   old: 120 527.184 120 527.184
   new: cB cA cA   11.1144e+025.3162e+02


 WARNING 8 [file ffbonded.itp, line 783]:
   Overriding Angle parameters.

   old: 117.3 527.184 117.3 527.184
   new: cB cB cA   11.2342e+025.3831e+02


 WARNING 9 [file ffbonded.itp, line 788]:
   Overriding Angle parameters.

   old: 120 418.4 120 418.4
   new: cA cA hA   11.1005e+023.8802e+02


 WARNING 10 [file ffbonded.itp, line 794]:
   Overriding Angle parameters.

   old: 120 418.4 120 418.4
   new: hA cA cB   11.1049e+023.9355e+02

 Aren't Atomtypes supposed to be case sensitive ?


Probably not, when pdb2gmx was designed.

Using a case-sensitive tool like sed (or perl, or python) to re-name cA
to LcA or something is probably the best solution. But don't break the
fixed-column requirements of your coordinate files!

Mark
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Re: [gmx-users] REMD run showing temperature range more than the equilibrated.

On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal suhani.nag...@gmail.comwrote:

 Hi all !

 well, I'm working on REMD with 96 replicas, with temperature range 280K to
 425.04K.

 The NVT equilibration works well and graphs plotted show almost the
 required temperature after equilibration.

 Then, after 3 ns of remd run , the edr - xvg files show initial
 temperature atleast 40 -50 units up , and then gradually reduces to it's
 temperature.

 for example
 replica 0 has 280 temperature , for initial 40 ps, it shows temperature up
 till 335K an then, decline.


Sounds like you're re-generating velocities, or mismatching input files.



 and around 21st to 22nd replica, the exchange probability is varying a lot
 from 20% to 60%.

 so, my queries are

  how to resolve this temperature issue and why is the exchange probability
 so abrupt at 21-22 replica ?


Can't say. Might even be real!

Mark
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RE: [gmx-users] Problems building gromacs 4.6

2013-06-07 Thread Colin Bannister

Mark,

Thanks for the response.  We use MKL for a lot of applications, and have had no 
problems, except with gromacs.  I wonder if there is a bug in cmake, as surely 
getting a segmentation fault can never be right ?

If anyone else has any ideas, I'd be grateful for them - I will try a build 
with FFTW3 for now.

Colin

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: 07 June 2013 15:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Problems building gromacs 4.6

On Fri, Jun 7, 2013 at 12:20 PM, colinbannister  
colin.bannis...@nottingham.ac.uk wrote:

 I am trying to build Gromacs 4.6 on a Linux machine, running 
 Scientific Linux 6.2.  I am doing an MPI build with Intel-MPI, and 
 Intel compilers, and MKL.

 Commands I issue to set environment, and run cmake (available as 
 cmake28)
 are:

 [cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler/64
 [cczcb@login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0
 [cczcb@login02 gromacs-build-nocuda]$ module load intel/mkl/64
 [cczcb@login02 gromacs-build-nocuda]$ export CC=mpicc
 [cczcb@login02 gromacs-build-nocuda]$ export CXX=mpicxx
 [cczcb@login02 gromacs-build-nocuda]$ mklvars_intel64.sh
 [cczcb@login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6 
 -DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON 
 -DGMX_FFT_LIBRARY=mkl

 -DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mk
 l/include

 -DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/
 lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/201
 1_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/inte
 l/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so

 This completes, but gives Segmentation fault messages at the end.  
 Output attached as 'cmake28.out'

 When I type 'make', it gets to 53% then gives a large number of 
 'undefined reference' errors, see 'make.out'.

 I have also tried only putting the libmkl_core.so library path as the 
 setting for MKL_LIBRARIES.  This avoids the Segmentation faults, but 
 again results in many undefined references, as you might expect.

 Any idea what could be happening here ?  Is Cmake messing up in 
 parsing the command in some way ?  Is there a different approach I 
 could use to build Gromacs ?


All that sounds very weird, and makes me wonder whether an MKL test program 
would compile on your system. Since the value of MKL is very limited, I would 
suggest compiling with FFTW for now.

GROMACS 4.6.2 streamlined the MKL build process greatly for icc = 11, but I 
would suggest waiting until GROMACS 4.6.3, because of a performance regression 
with MPI builds that we are working on fixing.

Cheers,

Mark



 Any assistance much appreciated!

 Colin

 cmake28.out 
 http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out
 make.out http://gromacs.5086.x6.nabble.com/file/n5008889/make.out




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Re: [gmx-users] Problems building gromacs 4.6

On Fri, Jun 7, 2013 at 5:22 PM, Colin Bannister 
colin.bannis...@nottingham.ac.uk wrote:

 Mark,

 Thanks for the response.  We use MKL for a lot of applications, and have
 had no problems, except with gromacs.


Because of the historical pain of specifying the MKL link configuration,
the ease of use of FFTW, and the very small benefit MKL has seemed to
provide, it's never been a priority for GROMACS. The icc -mkl flag makes
life much easier, and future GROMACS versions will use it.

 I wonder if there is a bug in cmake, as surely getting a segmentation
 fault can never be right ?


I've never seen CMake segfault.

If anyone else has any ideas, I'd be grateful for them - I will try a build
 with FFTW3 for now.


Other than try a new CMake, no.

Mark



 Colin

 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Mark Abraham
 Sent: 07 June 2013 15:44
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] Problems building gromacs 4.6

 On Fri, Jun 7, 2013 at 12:20 PM, colinbannister 
 colin.bannis...@nottingham.ac.uk wrote:

  I am trying to build Gromacs 4.6 on a Linux machine, running
  Scientific Linux 6.2.  I am doing an MPI build with Intel-MPI, and
  Intel compilers, and MKL.
 
  Commands I issue to set environment, and run cmake (available as
  cmake28)
  are:
 
  [cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler/64
  [cczcb@login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0
  [cczcb@login02 gromacs-build-nocuda]$ module load intel/mkl/64
  [cczcb@login02 gromacs-build-nocuda]$ export CC=mpicc
  [cczcb@login02 gromacs-build-nocuda]$ export CXX=mpicxx
  [cczcb@login02 gromacs-build-nocuda]$ mklvars_intel64.sh
  [cczcb@login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6
  -DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON
  -DGMX_FFT_LIBRARY=mkl
 
  -DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mk
  l/include
 
  -DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/
  lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/201
  1_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/inte
  l/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so
 
  This completes, but gives Segmentation fault messages at the end.
  Output attached as 'cmake28.out'
 
  When I type 'make', it gets to 53% then gives a large number of
  'undefined reference' errors, see 'make.out'.
 
  I have also tried only putting the libmkl_core.so library path as the
  setting for MKL_LIBRARIES.  This avoids the Segmentation faults, but
  again results in many undefined references, as you might expect.
 
  Any idea what could be happening here ?  Is Cmake messing up in
  parsing the command in some way ?  Is there a different approach I
  could use to build Gromacs ?
 

 All that sounds very weird, and makes me wonder whether an MKL test
 program would compile on your system. Since the value of MKL is very
 limited, I would suggest compiling with FFTW for now.

 GROMACS 4.6.2 streamlined the MKL build process greatly for icc = 11, but
 I would suggest waiting until GROMACS 4.6.3, because of a performance
 regression with MPI builds that we are working on fixing.

 Cheers,

 Mark


 
  Any assistance much appreciated!
 
  Colin
 
  cmake28.out
  http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out
  make.out http://gromacs.5086.x6.nabble.com/file/n5008889/make.out
 
 
 
 
  --
  View this message in context:
  http://gromacs.5086.x6.nabble.com/Problems-building-gromacs-4-6-tp5008
  889.html Sent from the GROMACS Users Forum mailing list archive at
  Nabble.com.
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[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

2013-06-07 Thread Amil Anderson

Roland,

I have now run the regression test on my installation and it all fails for
runmd (segmentation fault).  Don't see that anything else is being tested. 

I've placed the output of the make check  (Make_check.out) at

https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP

I'll copy the first part here to give you a taste of it:

---
[softwaremgmt@warp2-login build]$ more make_check.out
[ 64%] Built target gmx
[ 64%] Built target gmxfftw
[ 76%] Built target md
[ 92%] Built target gmxana
[ 92%] Built target editconf
[ 97%] Built target gmxpreprocess
[ 97%] Built target grompp
[ 98%] Built target pdb2gmx
[ 98%] Built target gmxcheck
[100%] Built target mdrun
[100%] Built target gmxtests
Test project /shared/software/temp/gromacs-4.6.1/build
Start 1: regressiontests/simple
1/5 Test #1: regressiontests/simple ...***Failed0.83 sec
sh: line 1: 11622 Segmentation fault  mdrun -notunepme -table ../table
-tabl
ep ../tablep  mdrun.out 21

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p mdrun.out 21' was 139
No mdrun output files.
FAILED. Check mdrun.out, md.log files in angles1
sh: line 1: 11628 Segmentation fault  mdrun -notunepme -table ../table
-tabl
ep ../tablep  mdrun.out 21

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p mdrun.out 21' was 139
No mdrun output files.
FAILED. Check mdrun.out, md.log files in angles125
sh: line 1: 11637 Segmentation fault  mdrun -notunepme -table ../table
-tabl
ep ../tablep -pd  mdrun.out 21

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p -pd mdrun.out 21' was 139
No mdrun output files.
FAILED. Check mdrun.out, md.log files in bham

...

0% tests passed, 5 tests failed out of 5

Total Test time (real) =  29.58 sec

The following tests FAILED:
  1 - regressiontests/simple (Failed)
  2 - regressiontests/complex (Failed)
  3 - regressiontests/kernel (Failed)
  4 - regressiontests/freeenergy (Failed)
  5 - regressiontests/pdb2gmx (Failed)


Amil





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Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

2013-06-07 Thread Roland Schulz

Amil,

would it be possible for you to compile with a different compiler?
Ideally gcc 4.7.3. Alternative could you send us the stack for when it
crashes?
For that you need to:
- compile with debug -DCMAKE_BUILD_TYPE=Debug
- run under gdb gdb --arg /path/to/mdrun {your mdrun arguments}
- enter bt after it crashes

Roland

On Fri, Jun 7, 2013 at 12:19 PM, Amil Anderson aander...@wittenberg.edu wrote:
 Roland,

 I have now run the regression test on my installation and it all fails for
 runmd (segmentation fault).  Don't see that anything else is being tested.

 I've placed the output of the make check  (Make_check.out) at

 https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP

 I'll copy the first part here to give you a taste of it:

 ---
 [softwaremgmt@warp2-login build]$ more make_check.out
 [ 64%] Built target gmx
 [ 64%] Built target gmxfftw
 [ 76%] Built target md
 [ 92%] Built target gmxana
 [ 92%] Built target editconf
 [ 97%] Built target gmxpreprocess
 [ 97%] Built target grompp
 [ 98%] Built target pdb2gmx
 [ 98%] Built target gmxcheck
 [100%] Built target mdrun
 [100%] Built target gmxtests
 Test project /shared/software/temp/gromacs-4.6.1/build
 Start 1: regressiontests/simple
 1/5 Test #1: regressiontests/simple ...***Failed0.83 sec
 sh: line 1: 11622 Segmentation fault  mdrun -notunepme -table ../table
 -tabl
 ep ../tablep  mdrun.out 21

 Abnormal return value for ' mdrun-notunepme -table ../table -tablep
 ../table
 p mdrun.out 21' was 139
 No mdrun output files.
 FAILED. Check mdrun.out, md.log files in angles1
 sh: line 1: 11628 Segmentation fault  mdrun -notunepme -table ../table
 -tabl
 ep ../tablep  mdrun.out 21

 Abnormal return value for ' mdrun-notunepme -table ../table -tablep
 ../table
 p mdrun.out 21' was 139
 No mdrun output files.
 FAILED. Check mdrun.out, md.log files in angles125
 sh: line 1: 11637 Segmentation fault  mdrun -notunepme -table ../table
 -tabl
 ep ../tablep -pd  mdrun.out 21

 Abnormal return value for ' mdrun-notunepme -table ../table -tablep
 ../table
 p -pd mdrun.out 21' was 139
 No mdrun output files.
 FAILED. Check mdrun.out, md.log files in bham

 ...

 0% tests passed, 5 tests failed out of 5

 Total Test time (real) =  29.58 sec

 The following tests FAILED:
   1 - regressiontests/simple (Failed)
   2 - regressiontests/complex (Failed)
   3 - regressiontests/kernel (Failed)
   4 - regressiontests/freeenergy (Failed)
   5 - regressiontests/pdb2gmx (Failed)
 

 Amil





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Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Running Amil's .tpr, the next output is from our CPU detection machinery.
While the Xeon 5500 is not exactly new, AFAIK there should be no reason for
the detection to fail. But the stack trace will tell.

Mark


On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz rol...@utk.edu wrote:

 Amil,

 would it be possible for you to compile with a different compiler?
 Ideally gcc 4.7.3. Alternative could you send us the stack for when it
 crashes?
 For that you need to:
 - compile with debug -DCMAKE_BUILD_TYPE=Debug
 - run under gdb gdb --arg /path/to/mdrun {your mdrun arguments}
 - enter bt after it crashes

 Roland

 On Fri, Jun 7, 2013 at 12:19 PM, Amil Anderson aander...@wittenberg.edu
 wrote:
  Roland,
 
  I have now run the regression test on my installation and it all fails
 for
  runmd (segmentation fault).  Don't see that anything else is being
 tested.
 
  I've placed the output of the make check  (Make_check.out) at
 
  https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP
 
  I'll copy the first part here to give you a taste of it:
 
 
 ---
  [softwaremgmt@warp2-login build]$ more make_check.out
  [ 64%] Built target gmx
  [ 64%] Built target gmxfftw
  [ 76%] Built target md
  [ 92%] Built target gmxana
  [ 92%] Built target editconf
  [ 97%] Built target gmxpreprocess
  [ 97%] Built target grompp
  [ 98%] Built target pdb2gmx
  [ 98%] Built target gmxcheck
  [100%] Built target mdrun
  [100%] Built target gmxtests
  Test project /shared/software/temp/gromacs-4.6.1/build
  Start 1: regressiontests/simple
  1/5 Test #1: regressiontests/simple ...***Failed0.83 sec
  sh: line 1: 11622 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in angles1
  sh: line 1: 11628 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in angles125
  sh: line 1: 11637 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep -pd  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p -pd mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in bham
 
  ...
 
  0% tests passed, 5 tests failed out of 5
 
  Total Test time (real) =  29.58 sec
 
  The following tests FAILED:
1 - regressiontests/simple (Failed)
2 - regressiontests/complex (Failed)
3 - regressiontests/kernel (Failed)
4 - regressiontests/freeenergy (Failed)
5 - regressiontests/pdb2gmx (Failed)
 
 
 
  Amil
 
 
 
 
 
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 http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008902.html
  Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] User-define non bonded table




On 6/7/13 10:33 AM, Steven Neumann wrote:

It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.


That may be an erroneous statement.  Within very short distances, you will have 
nearly infinite forces, so zeroes are used instead since these distances should 
never occur.  There's nothing wrong, per se, with entering really huge numbers 
for short distances.



The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some values so the potential will equal zero?



The table entries must continue until rc + 1 nm, where rc is the longest cutoff 
specified in the .mdp file.


-Justin



On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann s.neuman...@gmail.comwrote:





On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:




On 6/7/13 8:21 AM, Steven Neumann wrote:


Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x)
and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :

[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

or

[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05

Or maybe both?



Try the tutorial first and make sure you can replicate it.  If you're
just looking to tweak C6 and C12 parameters, there's no need for tabulated
functions at all.

-Justin




I want to change function g(x) to use Chandler Anderson potential so g(x)
= 1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?





On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:




On 6/7/13 7:36 AM, Steven Neumann wrote:

  Thank you, just getting into this. I just dont understand why they

start
from x=0.04? Why not 0.02 or sth else?


  You can start the table from whatever value of x that you like, but

at a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.

-Justin


   On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena


maruthi.s...@gmail.comwrote:

 Hi Neumann,


   You  can use tabulated potential option
in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/
Tabulated_Potentialshttp://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials
http://**www.gromacs.org/Documentation/**
How-tos/Tabulated_Potentialshttp://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials





Thanks,
Mohan


On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com

  wrote:




   Dear Gmx Users,



I want to specify a table to mdrun for non bonded parameters. I wish
to

  set


  it up for all atoms with same potential. Is there any example of the


  table


  like this? I want use my specific potential so table should have two

columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
right?
How can I tell gromacs to use it for all interactions?

Thanks

Steven
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Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

2013-06-07 Thread Roland Schulz

On Fri, Jun 7, 2013 at 2:06 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
 Running Amil's .tpr, the next output is from our CPU detection machinery.
 While the Xeon 5500 is not exactly new, AFAIK there should be no reason for
 the detection to fail. But the stack trace will tell.
Good point. Amil, please post the cmake output and the
CMakeFiles/CMakeError.log. Because the CPU detection probably also
already failed there if this is the case.

Roland


 Mark


 On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz rol...@utk.edu wrote:

 Amil,

 would it be possible for you to compile with a different compiler?
 Ideally gcc 4.7.3. Alternative could you send us the stack for when it
 crashes?
 For that you need to:
 - compile with debug -DCMAKE_BUILD_TYPE=Debug
 - run under gdb gdb --arg /path/to/mdrun {your mdrun arguments}
 - enter bt after it crashes

 Roland

 On Fri, Jun 7, 2013 at 12:19 PM, Amil Anderson aander...@wittenberg.edu
 wrote:
  Roland,
 
  I have now run the regression test on my installation and it all fails
 for
  runmd (segmentation fault).  Don't see that anything else is being
 tested.
 
  I've placed the output of the make check  (Make_check.out) at
 
  https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP
 
  I'll copy the first part here to give you a taste of it:
 
 
 ---
  [softwaremgmt@warp2-login build]$ more make_check.out
  [ 64%] Built target gmx
  [ 64%] Built target gmxfftw
  [ 76%] Built target md
  [ 92%] Built target gmxana
  [ 92%] Built target editconf
  [ 97%] Built target gmxpreprocess
  [ 97%] Built target grompp
  [ 98%] Built target pdb2gmx
  [ 98%] Built target gmxcheck
  [100%] Built target mdrun
  [100%] Built target gmxtests
  Test project /shared/software/temp/gromacs-4.6.1/build
  Start 1: regressiontests/simple
  1/5 Test #1: regressiontests/simple ...***Failed0.83 sec
  sh: line 1: 11622 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in angles1
  sh: line 1: 11628 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in angles125
  sh: line 1: 11637 Segmentation fault  mdrun -notunepme -table
 ../table
  -tabl
  ep ../tablep -pd  mdrun.out 21
 
  Abnormal return value for ' mdrun-notunepme -table ../table -tablep
  ../table
  p -pd mdrun.out 21' was 139
  No mdrun output files.
  FAILED. Check mdrun.out, md.log files in bham
 
  ...
 
  0% tests passed, 5 tests failed out of 5
 
  Total Test time (real) =  29.58 sec
 
  The following tests FAILED:
1 - regressiontests/simple (Failed)
2 - regressiontests/complex (Failed)
3 - regressiontests/kernel (Failed)
4 - regressiontests/freeenergy (Failed)
5 - regressiontests/pdb2gmx (Failed)
 
 
 
  Amil
 
 
 
 
 
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  View this message in context:
 http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008902.html
  Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Case sensitivity in atomtypes

2013-06-07 Thread Alan

I may not got the question properly but when I designed ACPYPE, I had
similar issues and for that reason I created this option:


-g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
file

So try your usual acpype command with -g option.

BTW, acpype -h can show you many more interesting options.

Alan


On 7 June 2013 15:55, Mark Abraham mark.j.abra...@gmail.com wrote:

 On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
 bat.demou...@gmail.comwrote:

  Hello GMX users,
 
  I have some troubles with overriding parameters. I have generated
  parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF,
  and Acpype. This forcefield contains atomtypes cA, cB for instance. When
 I
  include the bonded parameters in [bondtypes], [angletypes] sections of my
  topology, or alternatively in ffbonded.itp, grompp returns warning
  concerning overriding of bonds and angles involving CA, CB, HA, ...
 (AMBER
  atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA, ...).
 
  WARNING 1 [file ffbonded.itp, line 222]:
Overriding Bond parameters.
 
old: 0.137 435136 0.137 435136 --- VALUE FOR AMBER FF FOR
 CB-CB
  BOND
new: cB cB   11.3240e-014.9346e+05 --- VALUE FOR
 LIPID11
  cB-cB
 
 
  WARNING 2 [file ffbonded.itp, line 225]:
Overriding Bond parameters.
 
old: 0.1404 392459 0.1404 392459
new: cA cB   11.5080e-012.7472e+05
 
 
  WARNING 3 [file ffbonded.itp, line 227]:
Overriding Bond parameters.
 
old: 0.1381 357314 0.1381 357314
new: nA cA   11.4990e-012.4568e+05
 
 
  WARNING 4 [file ffbonded.itp, line 228]:
Overriding Bond parameters.
 
old: 0.108 307106 0.108 307106
new: cA hA   11.0920e-012.8225e+05
 
 
  WARNING 5 [file ffbonded.itp, line 229]:
Overriding Bond parameters.
 
old: 0.14 392459 0.14 392459
new: cA cA   11.5350e-012.5363e+05
 
 
  WARNING 6 [file ffbonded.itp, line 760]:
Overriding Angle parameters.
 
old: 120 527.184 120 527.184
new: cA cA cA   11.1063e+025.2894e+02
 
 
  WARNING 7 [file ffbonded.itp, line 773]:
Overriding Angle parameters.
 
old: 120 527.184 120 527.184
new: cB cA cA   11.1144e+025.3162e+02
 
 
  WARNING 8 [file ffbonded.itp, line 783]:
Overriding Angle parameters.
 
old: 117.3 527.184 117.3 527.184
new: cB cB cA   11.2342e+025.3831e+02
 
 
  WARNING 9 [file ffbonded.itp, line 788]:
Overriding Angle parameters.
 
old: 120 418.4 120 418.4
new: cA cA hA   11.1005e+023.8802e+02
 
 
  WARNING 10 [file ffbonded.itp, line 794]:
Overriding Angle parameters.
 
old: 120 418.4 120 418.4
new: hA cA cB   11.1049e+023.9355e+02
 
  Aren't Atomtypes supposed to be case sensitive ?
 

 Probably not, when pdb2gmx was designed.

 Using a case-sensitive tool like sed (or perl, or python) to re-name cA
 to LcA or something is probably the best solution. But don't break the
 fixed-column requirements of your coordinate files!

 Mark
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Re: [gmx-users] Case sensitivity in atomtypes

2013-06-07 Thread Baptiste Demoulin

Thank you for your answers,

I finally added l at the end of the names of the atoms, which seemed to
be the easiest solution. For most of the computation, having these
[bondtypes] like entries was not mandatory, but I wanted to import the
topologies in pDynamo, which requires such a database.

Thank you again !

Baptiste


2013/6/7 Alan alanwil...@gmail.com

 I may not got the question properly but when I designed ACPYPE, I had
 similar issues and for that reason I created this option:


 -g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
 file

 So try your usual acpype command with -g option.

 BTW, acpype -h can show you many more interesting options.

 Alan


 On 7 June 2013 15:55, Mark Abraham mark.j.abra...@gmail.com wrote:

  On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
  bat.demou...@gmail.comwrote:
 
   Hello GMX users,
  
   I have some troubles with overriding parameters. I have generated
   parameters for lipids using Lipid11 forcefield for AMBER, based on
 GAFF,
   and Acpype. This forcefield contains atomtypes cA, cB for instance.
 When
  I
   include the bonded parameters in [bondtypes], [angletypes] sections of
 my
   topology, or alternatively in ffbonded.itp, grompp returns warning
   concerning overriding of bonds and angles involving CA, CB, HA, ...
  (AMBER
   atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA,
 ...).
  
   WARNING 1 [file ffbonded.itp, line 222]:
 Overriding Bond parameters.
  
 old: 0.137 435136 0.137 435136 --- VALUE FOR AMBER FF FOR
  CB-CB
   BOND
 new: cB cB   11.3240e-014.9346e+05 --- VALUE FOR
  LIPID11
   cB-cB
  
  
   WARNING 2 [file ffbonded.itp, line 225]:
 Overriding Bond parameters.
  
 old: 0.1404 392459 0.1404 392459
 new: cA cB   11.5080e-012.7472e+05
  
  
   WARNING 3 [file ffbonded.itp, line 227]:
 Overriding Bond parameters.
  
 old: 0.1381 357314 0.1381 357314
 new: nA cA   11.4990e-012.4568e+05
  
  
   WARNING 4 [file ffbonded.itp, line 228]:
 Overriding Bond parameters.
  
 old: 0.108 307106 0.108 307106
 new: cA hA   11.0920e-012.8225e+05
  
  
   WARNING 5 [file ffbonded.itp, line 229]:
 Overriding Bond parameters.
  
 old: 0.14 392459 0.14 392459
 new: cA cA   11.5350e-012.5363e+05
  
  
   WARNING 6 [file ffbonded.itp, line 760]:
 Overriding Angle parameters.
  
 old: 120 527.184 120 527.184
 new: cA cA cA   11.1063e+025.2894e+02
  
  
   WARNING 7 [file ffbonded.itp, line 773]:
 Overriding Angle parameters.
  
 old: 120 527.184 120 527.184
 new: cB cA cA   11.1144e+025.3162e+02
  
  
   WARNING 8 [file ffbonded.itp, line 783]:
 Overriding Angle parameters.
  
 old: 117.3 527.184 117.3 527.184
 new: cB cB cA   11.2342e+025.3831e+02
  
  
   WARNING 9 [file ffbonded.itp, line 788]:
 Overriding Angle parameters.
  
 old: 120 418.4 120 418.4
 new: cA cA hA   11.1005e+023.8802e+02
  
  
   WARNING 10 [file ffbonded.itp, line 794]:
 Overriding Angle parameters.
  
 old: 120 418.4 120 418.4
 new: hA cA cB   11.1049e+023.9355e+02
  
   Aren't Atomtypes supposed to be case sensitive ?
  
 
  Probably not, when pdb2gmx was designed.
 
  Using a case-sensitive tool like sed (or perl, or python) to re-name cA
  to LcA or something is probably the best solution. But don't break the
  fixed-column requirements of your coordinate files!
 
  Mark
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[gmx-users] maining helix conformation

2013-06-07 Thread Sanku M

Hi,
  I have a pair of polypeptides which are generated as ideal helix. I want to 
carry out their assembly/dis-assembly simulation by maintaining the helicity of 
them.
I wonder which of the methods for retaining helicity is better :
1. use a harmonic restraints using [bonds] directive using type 6  among the 
backbone amide Hbond between i and i+4th residue.
2. Use dihedral restraint to maintain phi and Psi.
Any help will be appreciated. 
Thanks
Sanku
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Re: [gmx-users] maining helix conformation




On 6/7/13 8:43 PM, Sanku M wrote:

Hi,
   I have a pair of polypeptides which are generated as ideal helix. I want to 
carry out their assembly/dis-assembly simulation by maintaining the helicity of 
them.
I wonder which of the methods for retaining helicity is better :
1. use a harmonic restraints using [bonds] directive using type 6  among the 
backbone amide Hbond between i and i+4th residue.
2. Use dihedral restraint to maintain phi and Psi.
Any help will be appreciated.


Either should work.  Method 2 may be slightly more direct and less error-prone 
since the restraints can be easily written using genrestr.


-Justin

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Virginia Tech
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[gmx-users] changing the version of file

2013-06-07 Thread Souilem Safa

Dear Gromacs users,

I'm aiming to extract a frame file from a reduced trajectory, i did the
simulation on gromacs version 4.6.1 and I would like to do my analysis in
gromacs 4.5.6 for availability reasons.
When I entered my command , I got this error :
 reading tpx file (md.tpr) version 83 with version 73 program

Can any one help me how shoud I do to overcome this problem?
Many thanks
Safa
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Re: [gmx-users] changing the version of file