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
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 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] 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
wrote:

>  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  >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
> > --
> > 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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> >
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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 wrote:

> 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 wrote:


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
wrote:


  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 
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  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
>> wrote:
>>
>>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 >>
 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 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/Searchbefore
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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 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  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

wrote:

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 
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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--


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  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  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
>>>
 wrote:

 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 
>  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
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>
>> * Please search the archive at
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>> posting!
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>> >
>>
>>   --
>>
> gmx-users mailing listgmx-users@gromacs.org
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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
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.g

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 wrote:

> 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!
> >
> >
> >
> > --
> > View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-
> > linear-data-output-storage-possible-tp5008858.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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 wrote:

>
>
>
> On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul  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  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

> wrote:
>
> 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
>> > How-tos/Tabulated_Potentials
>> >
>>
>>
>> Thanks,
>> Mohan
>>
>>
>> On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann >
>>  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
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> >
>>>
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>>> >
>>>
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>>>
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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 
> make.out 
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Problems-building-gromacs-4-6-tp5008889.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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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
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> --
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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  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  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
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Getting-edr-file-data-as-a-generic-data-file-tp5008863.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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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 wrote:

> 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
wrote:

> 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 wrote:

> 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 
> 
> 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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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
> > 
> > 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.
> > --
> > 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.
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> any attachment.  Any

[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 2>&1

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p >mdrun.out 2>&1' 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 2>&1

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p >mdrun.out 2>&1' 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 2>&1

Abnormal return value for ' mdrun-notunepme -table ../table -tablep
../table
p -pd >mdrun.out 2>&1' 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  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 2>&1
>
> Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> ../table
> p >mdrun.out 2>&1' 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 2>&1
>
> Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> ../table
> p >mdrun.out 2>&1' 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 2>&1
>
> Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> ../table
> p -pd >mdrun.out 2>&1' 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
>
>
>
>
>
> --
> 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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>
>
>



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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  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 
> 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 2>&1
> >
> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> > ../table
> > p >mdrun.out 2>&1' 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 2>&1
> >
> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> > ../table
> > p >mdrun.out 2>&1' 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 2>&1
> >
> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
> > ../table
> > p -pd >mdrun.out 2>&1' 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
> >
> >
> >
> >
> >
> > --
> > 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.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> >
> >
> >
>
>
>
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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 wrote:





On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul  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  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


wrote:

 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 



   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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====


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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  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  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 
>> 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 2>&1
>> >
>> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
>> > ../table
>> > p >mdrun.out 2>&1' 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 2>&1
>> >
>> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
>> > ../table
>> > p >mdrun.out 2>&1' 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 2>&1
>> >
>> > Abnormal return value for ' mdrun-notunepme -table ../table -tablep
>> > ../table
>> > p -pd >mdrun.out 2>&1' 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
>> >
>> >
>> >
>> >
>> >
>> > --
>> > 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.
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
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>> >
>> >
>> >
>> >
>>
>>
>>
>> --
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>> 865-241-1537, ORNL PO BOX 2008 MS6309
>> --
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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  wrote:

> On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
> wrote:
>
> > 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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-- 
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Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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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 

> 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  wrote:
>
> > On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
> > wrote:
> >
> > > 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
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
> --
> gmx-users mailing listgmx-users@gromacs.org
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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

--


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


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[gmx-users] 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