Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[Alex]

I answered your question earlier: Gromacs forcefields do not do that, so 
you cannot have a reasonable model of a metal surface. Further, E = 0 
only holds for a perfectly flat metal surface in the macroscopic sense 
and the actual picture is a bit more intricate.
Your second question probably has to do with basic forces arising from 
solid-fluid interactions (i.e. drag) and of course they would come out 
of any reasonable forcefield.


Alex

On 3/24/2018 4:45 PM, Amin Rouy wrote:

Dear Mark, I have already checked the manual then wrote the question here.

Dear Alex, what I mean is simply when we have a metal surface in contact
with charged fluid, boundary condition at surface E=0 leads to different
result of Poisson equation (image charges method). So does Gromacs do that?

Dear David, it is a fluid dynamic concept. When an object moves inside a
fluid, it feels some force (hydrodynamic force), and if more than one body
moving in the fluid they feel some interactions due to each others
movement. So does Gromacs gives hydrodynamic properties on immersed objects
in a fluid?



On Sat, Mar 24, 2018 at 9:48 PM, David van der Spoel 
wrote:


Den 2018-03-24 kl. 20:29, skrev Amin Rouy:


Hi,

I have 2 questions please?

1- Is Gromacs able to simulate metallic system (Poisson equation should be
solved at the surface)

2- is Gromacs able to calculate hydrodynamic interactions?


What are hydrodynamic interactions? This is a serious question.

My anwsers would be
2a) there is no such thing as a hydrodynamic "interaction"
2b) yes, gromacs can calculate transport properties such as diffusion
(equilibrium MD simulations) and viscosity (equilibrium and non-equilibrium
MD) and effective interactions between particles (through
potential-of-mean-force calculations). All of these are well established
techniques. The accuracy of the results depends as always on the force
field and the sampling.




thanks.


On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:

Hi,

I have 2 questions please?

1- Does Gromacs ability to solve Poisson equation, e.g. boundary
condition
on metal surface?

2- is Gromacs able to calculate hydrodynamic interactions?

thanks



--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[Amin Rouy]

Dear Mark, I have already checked the manual then wrote the question here.

Dear Alex, what I mean is simply when we have a metal surface in contact
with charged fluid, boundary condition at surface E=0 leads to different
result of Poisson equation (image charges method). So does Gromacs do that?

Dear David, it is a fluid dynamic concept. When an object moves inside a
fluid, it feels some force (hydrodynamic force), and if more than one body
moving in the fluid they feel some interactions due to each others
movement. So does Gromacs gives hydrodynamic properties on immersed objects
in a fluid?



On Sat, Mar 24, 2018 at 9:48 PM, David van der Spoel 
wrote:

> Den 2018-03-24 kl. 20:29, skrev Amin Rouy:
>
>> Hi,
>>
>> I have 2 questions please?
>>
>> 1- Is Gromacs able to simulate metallic system (Poisson equation should be
>> solved at the surface)
>>
>> 2- is Gromacs able to calculate hydrodynamic interactions?
>>
> What are hydrodynamic interactions? This is a serious question.
>
> My anwsers would be
> 2a) there is no such thing as a hydrodynamic "interaction"
> 2b) yes, gromacs can calculate transport properties such as diffusion
> (equilibrium MD simulations) and viscosity (equilibrium and non-equilibrium
> MD) and effective interactions between particles (through
> potential-of-mean-force calculations). All of these are well established
> techniques. The accuracy of the results depends as always on the force
> field and the sampling.
>
>
>
>> thanks.
>>
>>
>> On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:
>>
>> Hi,
>>>
>>> I have 2 questions please?
>>>
>>> 1- Does Gromacs ability to solve Poisson equation, e.g. boundary
>>> condition
>>> on metal surface?
>>>
>>> 2- is Gromacs able to calculate hydrodynamic interactions?
>>>
>>> thanks
>>>
>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] How to understand compressed-x-precision?

[Dawid das]

OK, thank you.

2018-03-24 22:02 GMT+01:00 Mark Abraham :

> Hi,
>
> That coordinates will have three digits of precision, e.g from multiplying
> by 1000, truncating to an integer and dividing by 1000 again.
>
> Mark
>
> On Sat, Mar 24, 2018, 21:58 Dawid das  wrote:
>
> > Dear Gromacs Users,
> >
> > As in the topic. How do I understand default precision of 1000 for
> > *compressed-x-precision* option?
> >
> > Best wishes,
> > Dawid Grabarek
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] Different results from gmx rms

[Dawid das]

I checked again and it didn't.

2018-03-24 21:58 GMT+01:00 Mark Abraham :

> Hi,
>
> Did gmx rms warn you suitably that it was making guesses about masses?
>
> Mark
>
> On Sat, Mar 24, 2018, 21:07 Dawid das  wrote:
>
> > Thank you Justin. In fact, editconf gave me .gro file with the same
> > coordinates as starting ones, so it must be due to masses.
> >
> > I checked again with -nowm and now both start-cryst-structure.gro and
> > minimize.tpr give me the same RMS, so these must be
> > the masses. I added my own amino acid residue definition and plausibly
> for
> > my new non-hydrogen atoms, the guessed mass
> > is that of carbon, while there are carbon, nitrogen, oxygen atoms.
> >
> > Best regards,
> > Dawid
> >
> > 2018-03-24 20:56 GMT+01:00 Justin Lemkul :
> >
> > >
> > >
> > > On 3/24/18 3:55 PM, Dawid das wrote:
> > >
> > >> Hi,
> > >> well actually I used the same file to make minimize.tpr
> > >>
> > >
> > > Verify that the coordinates are the same by using editconf to extract
> > > coordinates from the .tpr file in .gro format, and then if they are the
> > > same, the difference likely comes from the fact that masses are guessed
> > > when providing a .gro file as a reference, whereas the precise values
> are
> > > used when providing a .tpr file. There may be small differences there
> > with
> > > respect to precision, which therefore influences the least-squares
> > fitting.
> > >
> > > -Justin
> > >
> > >
> > > Dawid
> > >>
> > >> 2018-03-24 20:51 GMT+01:00 Mark Abraham :
> > >>
> > >> Hi,
> > >>>
> > >>> That depends on what you used to make minimize.tpr. If it's different
> > >>> from
> > >>> the gro file then the rmsd will differ.
> > >>>
> > >>> Mark
> > >>>
> > >>> On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:
> > >>>
> > >>> Dear Gromacs Users,
> > 
> >  I get a bit different RMS when I use either minimize.tpr or
> >  start-crystal-structure.gro as a reference structure.
> >  This is definitely not because some atoms come across the
> >  boundary as simulation progresses (I checked that). What could be
> >  the reason? Does minimize.tpr use a different reference structure
> >  or has a different precision than start-crystal-structure.gro which
> >  was created starting from PDB crystal structure?
> > 
> >  Best wishes,
> >  Dawid Grabarek
> >  --
> >  Gromacs Users mailing list
> > 
> >  * Please search the archive at
> >  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >  posting!
> > 
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> > 
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> or
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> > 
> >  --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at http://www.gromacs.org/
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> > >>>
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> or
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> > >>>
> > >>>
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==
> > >
> > >
> > > --
> > > Gromacs Users mailing list
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Re: [gmx-users] How to understand compressed-x-precision?

[Mark Abraham]

Hi,

That coordinates will have three digits of precision, e.g from multiplying
by 1000, truncating to an integer and dividing by 1000 again.

Mark

On Sat, Mar 24, 2018, 21:58 Dawid das  wrote:

> Dear Gromacs Users,
>
> As in the topic. How do I understand default precision of 1000 for
> *compressed-x-precision* option?
>
> Best wishes,
> Dawid Grabarek
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Different results from gmx rms

[Mark Abraham]

Hi,

Did gmx rms warn you suitably that it was making guesses about masses?

Mark

On Sat, Mar 24, 2018, 21:07 Dawid das  wrote:

> Thank you Justin. In fact, editconf gave me .gro file with the same
> coordinates as starting ones, so it must be due to masses.
>
> I checked again with -nowm and now both start-cryst-structure.gro and
> minimize.tpr give me the same RMS, so these must be
> the masses. I added my own amino acid residue definition and plausibly for
> my new non-hydrogen atoms, the guessed mass
> is that of carbon, while there are carbon, nitrogen, oxygen atoms.
>
> Best regards,
> Dawid
>
> 2018-03-24 20:56 GMT+01:00 Justin Lemkul :
>
> >
> >
> > On 3/24/18 3:55 PM, Dawid das wrote:
> >
> >> Hi,
> >> well actually I used the same file to make minimize.tpr
> >>
> >
> > Verify that the coordinates are the same by using editconf to extract
> > coordinates from the .tpr file in .gro format, and then if they are the
> > same, the difference likely comes from the fact that masses are guessed
> > when providing a .gro file as a reference, whereas the precise values are
> > used when providing a .tpr file. There may be small differences there
> with
> > respect to precision, which therefore influences the least-squares
> fitting.
> >
> > -Justin
> >
> >
> > Dawid
> >>
> >> 2018-03-24 20:51 GMT+01:00 Mark Abraham :
> >>
> >> Hi,
> >>>
> >>> That depends on what you used to make minimize.tpr. If it's different
> >>> from
> >>> the gro file then the rmsd will differ.
> >>>
> >>> Mark
> >>>
> >>> On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:
> >>>
> >>> Dear Gromacs Users,
> 
>  I get a bit different RMS when I use either minimize.tpr or
>  start-crystal-structure.gro as a reference structure.
>  This is definitely not because some atoms come across the
>  boundary as simulation progresses (I checked that). What could be
>  the reason? Does minimize.tpr use a different reference structure
>  or has a different precision than start-crystal-structure.gro which
>  was created starting from PDB crystal structure?
> 
>  Best wishes,
>  Dawid Grabarek
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>  posting!
> 
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
>  * For (un)subscribe requests visit
>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>  send a mail to gmx-users-requ...@gromacs.org.
> 
>  --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/
> >>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
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> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==
> >
> >
> > --
> > Gromacs Users mailing list
> >
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[gmx-users] How to understand compressed-x-precision?

[Dawid das]

Dear Gromacs Users,

As in the topic. How do I understand default precision of 1000 for
*compressed-x-precision* option?

Best wishes,
Dawid Grabarek
-- 
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Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[David van der Spoel]

Den 2018-03-24 kl. 20:29, skrev Amin Rouy:

Hi,

I have 2 questions please?

1- Is Gromacs able to simulate metallic system (Poisson equation should be
solved at the surface)

2- is Gromacs able to calculate hydrodynamic interactions?

What are hydrodynamic interactions? This is a serious question.

My anwsers would be
2a) there is no such thing as a hydrodynamic "interaction"
2b) yes, gromacs can calculate transport properties such as diffusion 
(equilibrium MD simulations) and viscosity (equilibrium and 
non-equilibrium MD) and effective interactions between particles 
(through potential-of-mean-force calculations). All of these are well 
established techniques. The accuracy of the results depends as always on 
the force field and the sampling.





thanks.


On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:


Hi,

I have 2 questions please?

1- Does Gromacs ability to solve Poisson equation, e.g. boundary condition
on metal surface?

2- is Gromacs able to calculate hydrodynamic interactions?

thanks




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

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Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[Alex]

I don't think question 1 has an answer in the documentation, or any 
documentation ever written anywhere.


Representing metallic systems in MD does not mean "Poisson equation 
should be solved at the surface," because Poisson is to be solved 
self-consistently throughout any system always. If the question was 
about Gromacs being able to reveal Fermi gas polarization near surfaces 
by creating images, then the answer is no. There are papers on the 
subject though.


Alex


On 3/24/2018 2:02 PM, Mark Abraham wrote:

Hi,

This is a great question to answer by looking in the documentation, which
you'll need to do anyway if the answer is yes ;-)

Mark

On Sat, Mar 24, 2018, 20:30 Amin Rouy  wrote:


Hi,

I have 2 questions please?

1- Is Gromacs able to simulate metallic system (Poisson equation should be
solved at the surface)

2- is Gromacs able to calculate hydrodynamic interactions?

thanks.


On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:


Hi,

I have 2 questions please?

1- Does Gromacs ability to solve Poisson equation, e.g. boundary

condition

on metal surface?

2- is Gromacs able to calculate hydrodynamic interactions?

thanks


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Re: [gmx-users] Different results from gmx rms

[Dawid das]

Thank you Justin. In fact, editconf gave me .gro file with the same
coordinates as starting ones, so it must be due to masses.

I checked again with -nowm and now both start-cryst-structure.gro and
minimize.tpr give me the same RMS, so these must be
the masses. I added my own amino acid residue definition and plausibly for
my new non-hydrogen atoms, the guessed mass
is that of carbon, while there are carbon, nitrogen, oxygen atoms.

Best regards,
Dawid

2018-03-24 20:56 GMT+01:00 Justin Lemkul :

>
>
> On 3/24/18 3:55 PM, Dawid das wrote:
>
>> Hi,
>> well actually I used the same file to make minimize.tpr
>>
>
> Verify that the coordinates are the same by using editconf to extract
> coordinates from the .tpr file in .gro format, and then if they are the
> same, the difference likely comes from the fact that masses are guessed
> when providing a .gro file as a reference, whereas the precise values are
> used when providing a .tpr file. There may be small differences there with
> respect to precision, which therefore influences the least-squares fitting.
>
> -Justin
>
>
> Dawid
>>
>> 2018-03-24 20:51 GMT+01:00 Mark Abraham :
>>
>> Hi,
>>>
>>> That depends on what you used to make minimize.tpr. If it's different
>>> from
>>> the gro file then the rmsd will differ.
>>>
>>> Mark
>>>
>>> On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:
>>>
>>> Dear Gromacs Users,

 I get a bit different RMS when I use either minimize.tpr or
 start-crystal-structure.gro as a reference structure.
 This is definitely not because some atoms come across the
 boundary as simulation progresses (I checked that). What could be
 the reason? Does minimize.tpr use a different reference structure
 or has a different precision than start-crystal-structure.gro which
 was created starting from PDB crystal structure?

 Best wishes,
 Dawid Grabarek
 --
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 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>
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>
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Re: [gmx-users] Installation error

[Mark Abraham]

Hi,

No. You said you have fftw 3.3.7 so just let the cmake you have use it :-)

Mark

On Sat, Mar 24, 2018, 18:49 ali akgün  wrote:

> Should i use another version of cmake ?
> On Sat, Mar 24, 2018 at 3:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you have fftw 3.3.7, then you don't need to ask the GROMACS build
> system
> > to download and build fftw for you. The error is suggesting that the
> issue
> > is that your CMake build wasn't configured to be able to do the download
> > that your asking GROMACS to ask CMake to do.
> >
> > Mark
> >
> > On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:
> >
> > > Hello,
> > >
> > > I got an error in gromacs-5.0.7 installiation cmake part.
> > >
> > > My error is:
> > >
> > >
> > > Scanning dependencies of target fftwBuild
> > > Scanning dependencies of target mdrun_objlib
> > > Scanning dependencies of target view_objlib
> > > [  0%] Performing pre-download step for 'fftwBuild'
> > > [  0%] Creating directories for 'fftwBuild'
> > > -- downloading...
> > >  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
> > >
> > > dest='/home/ali/Downloads/gromacs-5.0.7/build/src/
> > contrib/fftw/fftw.tar.gz'
> > > CMake Error at fftw-download.cmake:9 (file):
> > >   file DOWNLOAD not supported by bootstrap cmake.
> > >
> > >
> > > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for
> > target
> > >
> > > 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> > fftwBuild-pre-download'
> > > failed
> > > make[2]: ***
> > >
> > > [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> > fftwBuild-pre-download]
> > > Error 1
> > > make[2]: *** Waiting for unfinished jobs
> > > CMakeFiles/Makefile2:1124: recipe for target
> > > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > > make[1]: *** Waiting for unfinished jobs
> > > [  1%] Building CXX object
> > > src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> > > [  1%] Built target view_objlib
> > > [  1%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> > > [  2%] Building CXX object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> > > [  2%] Built target mdrun_objlib
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > >
> > > How to fix this error?
> > >
> > > Cmake version is 3.11.0
> > > FFTW version is 3.3.7
> > >
> > > Thank you.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> > --
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Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[Mark Abraham]

Hi,

This is a great question to answer by looking in the documentation, which
you'll need to do anyway if the answer is yes ;-)

Mark

On Sat, Mar 24, 2018, 20:30 Amin Rouy  wrote:

> Hi,
>
> I have 2 questions please?
>
> 1- Is Gromacs able to simulate metallic system (Poisson equation should be
> solved at the surface)
>
> 2- is Gromacs able to calculate hydrodynamic interactions?
>
> thanks.
>
>
> On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:
>
> > Hi,
> >
> > I have 2 questions please?
> >
> > 1- Does Gromacs ability to solve Poisson equation, e.g. boundary
> condition
> > on metal surface?
> >
> > 2- is Gromacs able to calculate hydrodynamic interactions?
> >
> > thanks
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Different results from gmx rms

[Justin Lemkul]

On 3/24/18 3:55 PM, Dawid das wrote:

Hi,
well actually I used the same file to make minimize.tpr


Verify that the coordinates are the same by using editconf to extract 
coordinates from the .tpr file in .gro format, and then if they are the 
same, the difference likely comes from the fact that masses are guessed 
when providing a .gro file as a reference, whereas the precise values 
are used when providing a .tpr file. There may be small differences 
there with respect to precision, which therefore influences the 
least-squares fitting.


-Justin


Dawid

2018-03-24 20:51 GMT+01:00 Mark Abraham :


Hi,

That depends on what you used to make minimize.tpr. If it's different from
the gro file then the rmsd will differ.

Mark

On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:


Dear Gromacs Users,

I get a bit different RMS when I use either minimize.tpr or
start-crystal-structure.gro as a reference structure.
This is definitely not because some atoms come across the
boundary as simulation progresses (I checked that). What could be
the reason? Does minimize.tpr use a different reference structure
or has a different precision than start-crystal-structure.gro which
was created starting from PDB crystal structure?

Best wishes,
Dawid Grabarek
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--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Different results from gmx rms

[Dawid das]

Hi,
well actually I used the same file to make minimize.tpr

Dawid

2018-03-24 20:51 GMT+01:00 Mark Abraham :

> Hi,
>
> That depends on what you used to make minimize.tpr. If it's different from
> the gro file then the rmsd will differ.
>
> Mark
>
> On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:
>
> > Dear Gromacs Users,
> >
> > I get a bit different RMS when I use either minimize.tpr or
> > start-crystal-structure.gro as a reference structure.
> > This is definitely not because some atoms come across the
> > boundary as simulation progresses (I checked that). What could be
> > the reason? Does minimize.tpr use a different reference structure
> > or has a different precision than start-crystal-structure.gro which
> > was created starting from PDB crystal structure?
> >
> > Best wishes,
> > Dawid Grabarek
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Different results from gmx rms

[Mark Abraham]

Hi,

That depends on what you used to make minimize.tpr. If it's different from
the gro file then the rmsd will differ.

Mark

On Sat, Mar 24, 2018, 20:32 Dawid das  wrote:

> Dear Gromacs Users,
>
> I get a bit different RMS when I use either minimize.tpr or
> start-crystal-structure.gro as a reference structure.
> This is definitely not because some atoms come across the
> boundary as simulation progresses (I checked that). What could be
> the reason? Does minimize.tpr use a different reference structure
> or has a different precision than start-crystal-structure.gro which
> was created starting from PDB crystal structure?
>
> Best wishes,
> Dawid Grabarek
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Different results from gmx rms

[Dawid das]

Dear Gromacs Users,

I get a bit different RMS when I use either minimize.tpr or
start-crystal-structure.gro as a reference structure.
This is definitely not because some atoms come across the
boundary as simulation progresses (I checked that). What could be
the reason? Does minimize.tpr use a different reference structure
or has a different precision than start-crystal-structure.gro which
was created starting from PDB crystal structure?

Best wishes,
Dawid Grabarek
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Poisson equation, Hydrodynamic interaction

[Amin Rouy]

Hi,

I have 2 questions please?

1- Is Gromacs able to simulate metallic system (Poisson equation should be
solved at the surface)

2- is Gromacs able to calculate hydrodynamic interactions?

thanks.


On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy  wrote:

> Hi,
>
> I have 2 questions please?
>
> 1- Does Gromacs ability to solve Poisson equation, e.g. boundary condition
> on metal surface?
>
> 2- is Gromacs able to calculate hydrodynamic interactions?
>
> thanks
>
-- 
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Re: [gmx-users] -rtpo option for pdb2gmx

[Justin Lemkul]

On 3/24/18 12:19 AM, Robert König wrote:

Hello,
I try to use a modified OPLSAA forcefield with GROMACS 2018 and I get this 
error:

---
Program: gmx pdb2gmx, version 2018
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 535)

Fatal error:
Found rtp entries for 'ACE' in both 'aminoacids' and
'./oplsaa.ff/ffoplsgas.rtp'. If you want the first definition to override the
second one, set the -rtpo option of pdb2gmx.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

What is the -rtpo option of pdb2gmx and how can I use it? I didnt find 
documentation or discussion for that, where can I get it?


I don't think that's an actual option, so that error message needs to be 
corrected.


OPLS has "ACE" as an acetyl cap, so either pick a new name for your 
residue or generate a separate force field rather than trying to hack 
the existing one.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Installation error

[ali akgün]

Should i use another version of cmake ?
On Sat, Mar 24, 2018 at 3:05 PM, Mark Abraham 
wrote:

> Hi,
>
> If you have fftw 3.3.7, then you don't need to ask the GROMACS build system
> to download and build fftw for you. The error is suggesting that the issue
> is that your CMake build wasn't configured to be able to do the download
> that your asking GROMACS to ask CMake to do.
>
> Mark
>
> On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:
>
> > Hello,
> >
> > I got an error in gromacs-5.0.7 installiation cmake part.
> >
> > My error is:
> >
> >
> > Scanning dependencies of target fftwBuild
> > Scanning dependencies of target mdrun_objlib
> > Scanning dependencies of target view_objlib
> > [  0%] Performing pre-download step for 'fftwBuild'
> > [  0%] Creating directories for 'fftwBuild'
> > -- downloading...
> >  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
> >
> > dest='/home/ali/Downloads/gromacs-5.0.7/build/src/
> contrib/fftw/fftw.tar.gz'
> > CMake Error at fftw-download.cmake:9 (file):
> >   file DOWNLOAD not supported by bootstrap cmake.
> >
> >
> > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for
> target
> >
> > 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> fftwBuild-pre-download'
> > failed
> > make[2]: ***
> >
> > [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> fftwBuild-pre-download]
> > Error 1
> > make[2]: *** Waiting for unfinished jobs
> > CMakeFiles/Makefile2:1124: recipe for target
> > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > make[1]: *** Waiting for unfinished jobs
> > [  1%] Building CXX object
> > src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> > [  1%] Built target view_objlib
> > [  1%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> > [  2%] Building CXX object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> > [  2%] Built target mdrun_objlib
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> >
> > How to fix this error?
> >
> > Cmake version is 3.11.0
> > FFTW version is 3.3.7
> >
> > Thank you.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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Re: [gmx-users] cudaMallocHost filed: unknown error

[Mark Abraham]

Hi,

Looks like rogue behavior from the GPU driver's last workload, or something
like that. cudaMallocHost asks the driver to allocate memory on the CPU in
a special way, but for GROMACS that can never run into e.g. lack of
resources.

Mark

On Fri, Mar 23, 2018, 21:27 Christopher Neale 
wrote:

> Hello,
>
> I am running gromacs 5.1.2 on single nodes where the run is set to use 32
> cores and 4 GPUs. The run command is:
>
> mpirun -np 32 gmx_mpi mdrun -deffnm MD -maxh $maxh -dd 4 4 2 -npme 0
> -gpu_id  -ntomp 1 -notunepme
>
> Some of my runs die with this error:
> cudaMallocHost of size 1024128 bytes failed: unknown error
>
> Below is the relevant part of the .log file. Searching the internet didn't
> turn up any solutions. I'll contact sysadmins if you think this is likely
> some problem with the hardware or rogue jobs. In my testing, a collection
> of 24 jobs had 6 die with this same error message (including the "1024128
> bytes" and "pmalloc_cuda.cu, line: 70"). All on different nodes, and all
> those node next took repeat jobs that run fine. When the error occured, it
> was always right at the start of the run.
>
>
> Thank you for your help,
> Chris.
>
>
>
> Command line:
>   gmx_mpi mdrun -deffnm MD -maxh 0.9 -dd 4 4 2 -npme 0 -gpu_id
>  -ntomp 1 -notunepme
>
>
> Number of logical cores detected (72) does not match the number reported
> by OpenMP (2).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 36 cores, 72 logical cores, 4 compatible GPUs
> Hardware detected on host ko026.localdomain (the node of MPI rank 0):
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Xeon(R) CPU E5-2695 v4 @ 2.10GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>   GPU info:
> Number of GPUs detected: 4
> #0: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
> compatible
> #1: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
> compatible
> #2: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
> compatible
> #3: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
> compatible
>
> Reading file MD.tpr, VERSION 5.1.2 (single precision)
> Can not increase nstlist because verlet-buffer-tolerance is not set or used
> Using 32 MPI processes
> Using 1 OpenMP thread per MPI process
>
> On host ko026.localdomain 4 GPUs user-selected for this run.
> Mapping of GPU IDs to the 32 PP ranks in this node:
> 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3
>
> NOTE: You assigned GPUs to multiple MPI processes.
>
> NOTE: Your choice of number of MPI ranks and amount of resources results
> in using 1 OpenMP threads per rank, which is most likely inefficient. The
> optimum is usually between 2 and 6 threads per rank.
>
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>   application clocks of the detected Tesla P100-PCIE-16GB GPU to
> improve performance.
>   Recompile with the NVML library (compatible with the driver used) or
> set application clocks manually.
>
>
> ---
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /net/scratch3/cneale/exe/KODIAK/GROMACS/source/gromacs-5.1.2/src/gromacs/gmxlib/cuda_tools/
> pmalloc_cuda.cu, line: 70
>
> Fatal error:
> cudaMallocHost of size 1024128 bytes failed: unknown error
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Halting parallel program gmx mdrun on rank 31 out of 32
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31
>
>
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Re: [gmx-users] Installation error

[Mark Abraham]

Hi,

If you have fftw 3.3.7, then you don't need to ask the GROMACS build system
to download and build fftw for you. The error is suggesting that the issue
is that your CMake build wasn't configured to be able to do the download
that your asking GROMACS to ask CMake to do.

Mark

On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:

> Hello,
>
> I got an error in gromacs-5.0.7 installiation cmake part.
>
> My error is:
>
>
> Scanning dependencies of target fftwBuild
> Scanning dependencies of target mdrun_objlib
> Scanning dependencies of target view_objlib
> [  0%] Performing pre-download step for 'fftwBuild'
> [  0%] Creating directories for 'fftwBuild'
> -- downloading...
>  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
>
> dest='/home/ali/Downloads/gromacs-5.0.7/build/src/contrib/fftw/fftw.tar.gz'
> CMake Error at fftw-download.cmake:9 (file):
>   file DOWNLOAD not supported by bootstrap cmake.
>
>
> src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for target
>
> 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download'
> failed
> make[2]: ***
>
> [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> CMakeFiles/Makefile2:1124: recipe for target
> 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> [  1%] Building CXX object
> src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> [  1%] Built target view_objlib
> [  1%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> [  2%] Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> [  2%] Built target mdrun_objlib
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
>
>
> How to fix this error?
>
> Cmake version is 3.11.0
> FFTW version is 3.3.7
>
> Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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[gmx-users] Installation error

[ali akgün]

Hello,

I got an error in gromacs-5.0.7 installiation cmake part.

My error is:


Scanning dependencies of target fftwBuild
Scanning dependencies of target mdrun_objlib
Scanning dependencies of target view_objlib
[  0%] Performing pre-download step for 'fftwBuild'
[  0%] Creating directories for 'fftwBuild'
-- downloading...
 src='http://www.fftw.org/fftw-3.3.3.tar.gz'

dest='/home/ali/Downloads/gromacs-5.0.7/build/src/contrib/fftw/fftw.tar.gz'
CMake Error at fftw-download.cmake:9 (file):
  file DOWNLOAD not supported by bootstrap cmake.


src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for target
'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download'
failed
make[2]: ***
[src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download]
Error 1
make[2]: *** Waiting for unfinished jobs
CMakeFiles/Makefile2:1124: recipe for target
'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
[  1%] Building CXX object
src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
[  1%] Built target view_objlib
[  1%] Building C object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
[  2%] Building C object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
[  2%] Building C object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
[  2%] Building C object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
[  2%] Building CXX object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
[  2%] Building C object
src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
[  2%] Built target mdrun_objlib
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2


How to fix this error?

Cmake version is 3.11.0
FFTW version is 3.3.7

Thank you.
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