[gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

I have trouble in correctly setting cut-offs with Verlet scheme to match 
force-field specific settings.
It automatically adjusts cut-off and it looks like they change their 
values from ones recommended for the force field.

Is there a way to correct it and set up them properly?

The paper on FF lists 1.0 nm for short-range electrostatic and LJ 
interactions.

The cut-off of pairlists is 1.05 nm.

The forcefield is 99SB-ILDN and is present in GROMACS itself.
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[gmx-users] F4-Order-parameter

[sujithkakkat .]

Dear all,

 I am using GROMACS-4.6.5 for studying gas hydrates and related
systems.
A useful order parameter which indicates water to hydrate transition is the
F4 order parameter where F4 is related to the H--O--O--H dihedral angle for
a pair of water molecules

Exact expression for F4 can be found in Phys. Chem. Chem. Phys., 2015, 17,
9509-9518.

The g_hydorder tool in GROMACS refers to an order parameter different in
definition from the F4 parameter.  (P.-L. Chau and A.J. Hardwick, Mol.
Phys., 93, (1998), 511-518.)

It is found that F4 parameter is very frequently used in several works on
gas hydrates done using GROMACS (including the PCCP article mentioned
above). I was wondering whether it is possible for any version of GROMACS
to compute the value of F4 for my system (water + gas molecules). If not I
guess I would have to write a program to do the same.

Please comment.

Regards,

Sujith.
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Re: [gmx-users] correct rlist and Verlet scheme

[Hardy, Adam]

There are people more qualified than me to explain the fine details of this, 
but in brief:

Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if 
you rae using PME for the coulomb interactions), but by default it will adjust 
the neighbour list cut-off (rlist) to remain with a specified energy tolerance 
given by verlet-buffer-tolerance. You can overide this behaviour and manually 
set rlist by setting verlet-buffer-tolerance=-1. Whether you want to or not 
will depend on why the forcefield has specified that cut-off, it may well be to 
achieve the same purpose, which is to propely catch interactions between atoms 
which move in or out of the cut-off radii between rlist update steps.

Adam


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Timofey 
Tyugashev 
Sent: 12 February 2016 12:47
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] correct rlist and Verlet scheme

I have trouble in correctly setting cut-offs with Verlet scheme to match
force-field specific settings.
It automatically adjusts cut-off and it looks like they change their
values from ones recommended for the force field.
Is there a way to correct it and set up them properly?

The paper on FF lists 1.0 nm for short-range electrostatic and LJ
interactions.
The cut-off of pairlists is 1.05 nm.

The forcefield is 99SB-ILDN and is present in GROMACS itself.
--
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[gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Hardy, Adam]

Dear all,


I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine. 
This is using the xl compiler.


I recieve the error:


ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the 
target platform supports only STATIC libraries. Building it STATIC instead. 
This may lead to problems.
-- Configuring done
CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
  Objects of target "mdrun_objlib" referenced but is not an OBJECT library.

If I attempt to compile it, it fails:

Linking CXX executable ../../bin/mdrun_mpi_d
CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to 
`gmx_mdrun(int, char**)'

My cmake command is as follow:

export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
export FLAGS="-O3 -qarch=qp -qtune=qp"
export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/

cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF 
-DGMX_DOUBLE=ON \
  -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" 
-DGMX_BUILD_MDRUN_ONLY=ON  \
  -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
  -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off 
-DGMX_BUILD_MDRUN_ONLY=ON\
  -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C 
-DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx


I have managed to build for a similar BGQ machine without problems, but I've no 
idea if this problem lies within GROMACS or with this machine.


Many thanks,


Adam

---

Adam Hardy

PhD Student

Heriot Watt University

Edinburgh Campus, Riccarton

EH14 4AS

+441314513074

ah...@hw.ac.uk

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Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Mark Abraham]

Hi,

Do the cmake versions differ?

Mark

On Fri, 12 Feb 2016 12:44 Hardy, Adam  wrote:

> Dear all,
>
>
> I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
> machine. This is using the xl compiler.
>
>
> I recieve the error:
>
>
> ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but
> the target platform supports only STATIC libraries. Building it STATIC
> instead. This may lead to problems.
> -- Configuring done
> CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
>   Objects of target "mdrun_objlib" referenced but is not an OBJECT library.
>
> If I attempt to compile it, it fails:
>
> Linking CXX executable ../../bin/mdrun_mpi_d
> CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to
> `gmx_mdrun(int, char**)'
>
> My cmake command is as follow:
>
> export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
> export FLAGS="-O3 -qarch=qp -qtune=qp"
> export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
> export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/
>
> cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF
> -DGMX_DOUBLE=ON \
>   -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
> -DGMX_BUILD_MDRUN_ONLY=ON  \
>   -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
>   -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off
> -DGMX_BUILD_MDRUN_ONLY=ON\
>   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C
> -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx
>
>
> I have managed to build for a similar BGQ machine without problems, but
> I've no idea if this problem lies within GROMACS or with this machine.
>
>
> Many thanks,
>
>
> Adam
>
> ---
>
> Adam Hardy
>
> PhD Student
>
> Heriot Watt University
>
> Edinburgh Campus, Riccarton
>
> EH14 4AS
>
> +441314513074
>
> ah...@hw.ac.uk
>
> ---
> --
> 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.
>
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Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Hardy, Adam]

Hi Mark,

I was able to compile GROMACS on Marenostrum, the cmake version is "2.6-patch 
2".

On Fermi it failed, the cmake version is "2.8.8". 

This is not necassarily a fair comparison. I compiled using gnu on Marenostrum 
as I couldn't find the xl compiler oddly and wasn't feeling compelled to go 
looking for it. I'm using xl on Fermi as using gnu is another problem all 
together:

CMake Error at cmake/gmxManageSimd.cmake:390 (message):
  Cannot compile the requested IBM QPX intrinsics.  If you are compiling for
  BlueGene/Q with the XL compilers, use 'cmake ..
  -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool
  chain.

Despite the correct file being specified and I can see the path set correctly 
in the CMakeCache.txt. 

Adam

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: 12 February 2016 12:06
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hi,

Do the cmake versions differ?

Mark

On Fri, 12 Feb 2016 12:44 Hardy, Adam  wrote:

> Dear all,
>
>
> I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
> machine. This is using the xl compiler.
>
>
> I recieve the error:
>
>
> ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but
> the target platform supports only STATIC libraries. Building it STATIC
> instead. This may lead to problems.
> -- Configuring done
> CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
>   Objects of target "mdrun_objlib" referenced but is not an OBJECT library.
>
> If I attempt to compile it, it fails:
>
> Linking CXX executable ../../bin/mdrun_mpi_d
> CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to
> `gmx_mdrun(int, char**)'
>
> My cmake command is as follow:
>
> export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
> export FLAGS="-O3 -qarch=qp -qtune=qp"
> export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
> export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/
>
> cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF
> -DGMX_DOUBLE=ON \
>   -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
> -DGMX_BUILD_MDRUN_ONLY=ON  \
>   -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
>   -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off
> -DGMX_BUILD_MDRUN_ONLY=ON\
>   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C
> -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx
>
>
> I have managed to build for a similar BGQ machine without problems, but
> I've no idea if this problem lies within GROMACS or with this machine.
>
>
> Many thanks,
>
>
> Adam
>
> ---
>
> Adam Hardy
>
> PhD Student
>
> Heriot Watt University
>
> Edinburgh Campus, Riccarton
>
> EH14 4AS
>
> +441314513074
>
> ah...@hw.ac.uk
>
> ---
> --
> 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.
>
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Re: [gmx-users] correct rlist and Verlet scheme

[Mark Abraham]

Hi,

As Adam says, you want to understand the reason why the forcefield
specifies the settings it does. For example, until at least AMBER 2003,
their force field papers did not specify PME parameters more precisely than
"x nm cutoff was used." If PME was used at all. ;-) So you can be guided
also by the parameters reported by successful users of these forcefields,
particularly those of the various force field and software authors.

rlist is a free parameter so long as you choose it large enough to avoid
missing a significant number of interactions over the lifetime of the list
- but it affects performance strongly. rcoulomb can be varied for
equivalent accuracy if matching changes occur to PME parameters. VDW
parameters should generally follow the force field derivation precisely
(but add long-range corrections for dispersion) - GROMACS will not change
these. You should check out the background information in the reference
manual, sections 3.4.2 and 3.17.5

Mark

On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam  wrote:

> There are people more qualified than me to explain the fine details of
> this, but in brief:
>
> Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be
> adjusted if you rae using PME for the coulomb interactions), but by default
> it will adjust the neighbour list cut-off (rlist) to remain with a
> specified energy tolerance given by verlet-buffer-tolerance. You can
> overide this behaviour and manually set rlist by setting
> verlet-buffer-tolerance=-1. Whether you want to or not will depend on why
> the forcefield has specified that cut-off, it may well be to achieve the
> same purpose, which is to propely catch interactions between atoms which
> move in or out of the cut-off radii between rlist update steps.
>
> Adam
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Timofey
> Tyugashev 
> Sent: 12 February 2016 12:47
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] correct rlist and Verlet scheme
>
> I have trouble in correctly setting cut-offs with Verlet scheme to match
> force-field specific settings.
> It automatically adjusts cut-off and it looks like they change their
> values from ones recommended for the force field.
> Is there a way to correct it and set up them properly?
>
> The paper on FF lists 1.0 nm for short-range electrostatic and LJ
> interactions.
> The cut-off of pairlists is 1.05 nm.
>
> The forcefield is 99SB-ILDN and is present in GROMACS itself.
> --
> 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.
> --
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>
> * 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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Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Hardy, Adam]

Sorry for the confusion, yes, find and replace Marenostrum with Juqeen for most 
of that last mail. Just got some PRACE test accounts and I got myself confused.

The 2.6 version of cmake was from Marenostum before I’d loaded the proper 
module.

Try again:

Fermi (failed build, xl compiler) - cmake 2.8.8
Juqeen (successful, gnu compiler?) - cmake 2.8.10.2

I had, clearly not really knowing what I was doing, specified gnu for Juqueen 
but this seems to be getting overridden somehow, I’ll look into that but 
whatever happened my build worked.

There’s no other version of cmake I can find but I’ll contact the helpdesk and 
see if they can make one available. If you have any other suggestions I’d love 
to hear them, otherwise thanks for your input.

Adam


On 12/02/2016, 13:50, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on 
behalf of Mark Abraham"  wrote:




>Hi,
>
>On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam  wrote:
>
>> Hi Mark,
>>
>> I was able to compile GROMACS on Marenostrum, the cmake version is
>> "2.6-patch 2".
>>
>
>That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few
>versions now.
>
>On Fermi it failed, the cmake version is "2.8.8".
>>
>
>OK. I suggest you try a more recent version of CMake. I can build fine on
>Vesta and Juqueen with e.g. 2.8.12.2, but haven't tried 2.8.8. Object
>modules were a new feature in 2.8.8 (part of why we require that version)
>and perhaps had some issues that have been resolved later.
>
>This is not necassarily a fair comparison. I compiled using gnu on
>> Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling
>> compelled to go looking for it.
>
>
>Marenostrum isn't even BG/Q!
>
>
>> I'm using xl on Fermi as using gnu is another problem all together:
>>
>> CMake Error at cmake/gmxManageSimd.cmake:390 (message):
>>   Cannot compile the requested IBM QPX intrinsics.  If you are compiling
>> for
>>   BlueGene/Q with the XL compilers, use 'cmake ..
>>   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool
>>   chain.
>>
>> Despite the correct file being specified and I can see the path set
>> correctly in the CMakeCache.txt.
>>
>
>gcc's never been a supported compiler for GROMACS on BG/Q. Your reports
>suggest that you were compiling GROMACS 4.5 on Marenostrum.
>
>Mark
>
>
>> Adam
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
>> Abraham 
>> Sent: 12 February 2016 12:06
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q
>>
>> Hi,
>>
>> Do the cmake versions differ?
>>
>> Mark
>>
>> On Fri, 12 Feb 2016 12:44 Hardy, Adam  wrote:
>>
>> > Dear all,
>> >
>> >
>> > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
>> > machine. This is using the xl compiler.
>> >
>> >
>> > I recieve the error:
>> >
>> >
>> > ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but
>> > the target platform supports only STATIC libraries. Building it STATIC
>> > instead. This may lead to problems.
>> > -- Configuring done
>> > CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
>> >   Objects of target "mdrun_objlib" referenced but is not an OBJECT
>> library.
>> >
>> > If I attempt to compile it, it fails:
>> >
>> > Linking CXX executable ../../bin/mdrun_mpi_d
>> > CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to
>> > `gmx_mdrun(int, char**)'
>> >
>> > My cmake command is as follow:
>> >
>> > export
>> CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
>> > export FLAGS="-O3 -qarch=qp -qtune=qp"
>> > export
>> FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
>> > export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/
>> >
>> > cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF
>> > -DGMX_DOUBLE=ON \
>> >   -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
>> > -DGMX_BUILD_MDRUN_ONLY=ON  \
>> >   -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
>> >   -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off
>> > -DGMX_BUILD_MDRUN_ONLY=ON\
>> >   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C
>> > -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx
>> >
>> >
>> > I have managed to build for a similar BGQ machine without problems, but
>> > I've no idea if this problem lies within GROMACS or with this machine.
>> >
>> >
>> > Many thanks,
>> >
>> >
>> > Adam
>> >
>> > ---
>> >
>> > Adam Hardy
>> >
>> > PhD Student
>> >
>> > Heriot Watt University
>> >
>> > Edinburgh Campus, Riccarton
>> >
>> > EH14 4AS
>> >
>> > +441314513074
>> >
>> > ah...@hw.ac.uk
>> >
>> > ---
>> > --
>> > Gromacs 

[gmx-users] PMF of a single water molecule respect to a surface

[Alexander Alexander]

Dear Gromacs user,

I am calculation the PMF of a single water molecule to pull it away from
top of metallic surface along vacuum in the Z direction ,following the
Justin umbrella tutorial. I am only  interested in the behavior of PMF in
0.002 nm to 0.8 nm intervalon top of the surface, but I do not why the
population of the generated frames in this interval is really low and then
the result is so poor.

So, would you please let me know which parameter I should play around with?

I just tried 0.001 instead 0.01 as the "pull_coord1_rate" and simultaneously
3500 instead of 1000 as "pull_coord1_k", but the result got even worse.

Best regards,

Alex
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Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Mark Abraham]

Hi,

On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam  wrote:

> Hi Mark,
>
> I was able to compile GROMACS on Marenostrum, the cmake version is
> "2.6-patch 2".
>

That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few
versions now.

On Fermi it failed, the cmake version is "2.8.8".
>

OK. I suggest you try a more recent version of CMake. I can build fine on
Vesta and Juqueen with e.g. 2.8.12.2, but haven't tried 2.8.8. Object
modules were a new feature in 2.8.8 (part of why we require that version)
and perhaps had some issues that have been resolved later.

This is not necassarily a fair comparison. I compiled using gnu on
> Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling
> compelled to go looking for it.


Marenostrum isn't even BG/Q!


> I'm using xl on Fermi as using gnu is another problem all together:
>
> CMake Error at cmake/gmxManageSimd.cmake:390 (message):
>   Cannot compile the requested IBM QPX intrinsics.  If you are compiling
> for
>   BlueGene/Q with the XL compilers, use 'cmake ..
>   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool
>   chain.
>
> Despite the correct file being specified and I can see the path set
> correctly in the CMakeCache.txt.
>

gcc's never been a supported compiler for GROMACS on BG/Q. Your reports
suggest that you were compiling GROMACS 4.5 on Marenostrum.

Mark


> Adam
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 12 February 2016 12:06
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q
>
> Hi,
>
> Do the cmake versions differ?
>
> Mark
>
> On Fri, 12 Feb 2016 12:44 Hardy, Adam  wrote:
>
> > Dear all,
> >
> >
> > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
> > machine. This is using the xl compiler.
> >
> >
> > I recieve the error:
> >
> >
> > ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but
> > the target platform supports only STATIC libraries. Building it STATIC
> > instead. This may lead to problems.
> > -- Configuring done
> > CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
> >   Objects of target "mdrun_objlib" referenced but is not an OBJECT
> library.
> >
> > If I attempt to compile it, it fails:
> >
> > Linking CXX executable ../../bin/mdrun_mpi_d
> > CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to
> > `gmx_mdrun(int, char**)'
> >
> > My cmake command is as follow:
> >
> > export
> CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
> > export FLAGS="-O3 -qarch=qp -qtune=qp"
> > export
> FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
> > export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/
> >
> > cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF
> > -DGMX_DOUBLE=ON \
> >   -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
> > -DGMX_BUILD_MDRUN_ONLY=ON  \
> >   -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
> >   -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off
> > -DGMX_BUILD_MDRUN_ONLY=ON\
> >   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C
> > -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx
> >
> >
> > I have managed to build for a similar BGQ machine without problems, but
> > I've no idea if this problem lies within GROMACS or with this machine.
> >
> >
> > Many thanks,
> >
> >
> > Adam
> >
> > ---
> >
> > Adam Hardy
> >
> > PhD Student
> >
> > Heriot Watt University
> >
> > Edinburgh Campus, Riccarton
> >
> > EH14 4AS
> >
> > +441314513074
> >
> > ah...@hw.ac.uk
> >
> > ---
> > --
> > 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
>
> * For (un)subscribe requests visit
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> posting!
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> * For (un)subscribe requests visit
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> send a mail to 

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Irina Kosheleva]

Hello Adam
For me alcf scientist suggested  to compile with:
Use xl compilers in your .soft environment.
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include 
-DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a  
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" -DCMAKE_INSTALL_PREFIX=
 It does not work for me because I have trouble compiling libxml2 library - 
suspect that come from Gromacs cmake command parsing-  but if you do not care - 
it may work for you.
Irina.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Hardy, 
Adam
Sent: Friday, February 12, 2016 5:44 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Dear all,


I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine. 
This is using the xl compiler.


I recieve the error:


ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the 
target platform supports only STATIC libraries. Building it STATIC instead. 
This may lead to problems.
-- Configuring done
CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
  Objects of target "mdrun_objlib" referenced but is not an OBJECT library.

If I attempt to compile it, it fails:

Linking CXX executable ../../bin/mdrun_mpi_d
CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to 
`gmx_mdrun(int, char**)'

My cmake command is as follow:

export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
export FLAGS="-O3 -qarch=qp -qtune=qp"
export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/

cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF 
-DGMX_DOUBLE=ON \
  -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" 
-DGMX_BUILD_MDRUN_ONLY=ON  \
  -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
  -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off 
-DGMX_BUILD_MDRUN_ONLY=ON\
  -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C 
-DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx


I have managed to build for a similar BGQ machine without problems, but I've no 
idea if this problem lies within GROMACS or with this machine.


Many thanks,


Adam

---

Adam Hardy

PhD Student

Heriot Watt University

Edinburgh Campus, Riccarton

EH14 4AS

+441314513074

ah...@hw.ac.uk

---
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[gmx-users] Installation problem

[Prof. Eddie]

Hi All,
I'm trying to install GROMACS 5.1.2 on ubuntu 14.04 LTS. I used:
cmake .. -DGMX_GPU=on -DGMX_USE_OPENCL=on -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON

Everything went fine, but make ended with:

[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/__/external/thread_mpi/src/once.c.o
[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
Linking CXX shared library ../../lib/libgromacs.so
[100%] Built target libgromacs
Scanning dependencies of target template
[100%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
eddie@heartofgold:~/bin/gromacs-5.1.2/build$ ^C
eddie@heartofgold:~/bin/gromacs-5.1.2/build$ make
[  0%] Built target fftwBuild
[100%] Built target libgromacs
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Any help would be very welcome! Thanks,
Eddie
-- 
_
Edward Ackad, Ph.D 
Assistant Professor of Physics
Computational Nanophotonics/Biophysics
Southern Illinois University Edwardsville
(618) 650-2390
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Re: [gmx-users] add parameter

[Malihe Hasanzadeh]

Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of parameters for dihedral;* Proper* and* Improper *dihedral
that the proper types have* scale=1, 2 or 3 *and* periodicity=**1, 2
or 3. *Since
some of *Proper types* are the same with different Phase, V and Periodicity
number, so I think, I should add all of them ( proper and improper
parameters) in second part with func=9 and ignore scale number for *Proper
types*. Because when I add them in first part with func=4 gave error. I see
manual but I couldn't find where do I add them.

for example:

*Proper types*
dihedral types   scaling  phase
V(kj/mol)periodicity

O   C   OQ  HQ 1   0.0  7.9496
 1  ;
O   C   OQ  HQ 1180.0  9.6232
2  ;

*Improper types*
dihedral types phase
V(kj/mol)periodicity

CA   CA   C  HQ 180.0  9.6232
2  ;

Could you please help me , where do I add the parameters of proper and
improper types in forcefield and what is the func number for them?
Thanks
Malihe







On Fri, Feb 12, 2016 at 5:12 AM, Justin Lemkul  wrote:

>
>
> On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:
>
>> Hi
>> I have three water molecules and one new residue that I want to add their
>> parameters to force field Amber99sb. One of water molecules has only one
>> hydrogen, and since I want to prevent from replacing with SOL in solvation
>> step, So I define them as new residue in .rtp file:
>>
>> [ INN ]
>>   [ atoms ]
>> H1H   0.384620 1
>>  OO  -0.671930 2
>> H2H   0.384620 3
>>
>>
>> [ INT ]
>>   [ atoms ]
>> H1H   0.286310 1
>>  OO  -0.341910 2
>> H2H   0.286310 3
>>
>>
>> [ INB ]
>>   [ atoms ]
>> H1H   0.477860 1
>>  OO  -1.092580 2
>> Also define them in .dat file as Protein  and in .hdb file as below:
>>
>>
> Defining these residues as protein is not necessary.
>
> INN2
>> 17H1O
>> 17H2O
>> INT2
>> 17H1O
>> 17H2O
>> INB1
>> 17H1O
>>
>> But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
>> gives segmentation fault! when I remove their parameters in .hdb file, it
>> is done but without any hydrogen for them, just three oxygen atoms in
>> em.gro!
>>
>>
> This is because you would have had to invoke -missing with pdb2gmx and
> yield something totally useless.
>
> Immediate seg faults are indicative of complete instability.  Note that
> none of your .rtp entries have [bonds] defined, so you probably just have
> particles very close to one another (e.g. as they would be in a real
> molecule) but no covalent attachment, so they likely just fly apart.
>
> Also I have another problem with that new residue, this residue is like a
>> Lys but has two carbonyl groups binded to extra carbon instead of amino
>> group in Lys. So I used Lys parameters for that and add some bonds and
>> atoms to it:
>>
>> [ NEW ] ;
>>   [ atoms ]
>>  N   N
>>  H   H
>> CA   CT
>> HAH1
>> CB   CT
>>HB1   HC
>>HB2   HC
>> CG  CT
>>HG1  H
>>HG2  H
>> CD  CT
>>HD1  HC
>>HD2  HC
>> CE  CT
>>HE1  HP
>>HE2  HP
>> NZ  N
>> HZ  H
>> CX  C
>>OQ1 O
>>OQ2 O
>>  C  C
>>  O  O
>>   [ bonds ]
>>   N H
>>   NCA
>>  CAHA
>>  CACB
>>  CA C
>>  CB   HB1
>>  CB   HB2
>>  CBCG
>>  CG   HG1
>>  CG   HG2
>>  CGCD
>>  CD   HD1
>>  CD   HD2
>>  CDCE
>>  CE   HE1
>>  CE   HE2
>>  CENZ
>>  NZHZ
>>  NZCX
>>   C O
>>  CX   OQ1
>>  CX   OQ2
>>   [ impropers ]
>>  -CCA N H
>>  CA+N C O
>> when I added only atoms parameters in .rtp file, finally in em.gro file
>> there wasn't any bond between atoms of new residue and when I added bond
>>
>
> As you should expect.  See above.  [bonds] is a mandatory directive (which
> is also stated clearly in the manual).
>
> parameters also, in grompp gives 10 error about "default angel and
>> dihedral"! I find the number of angels in .top file and added them to
>> ffbonded.itp, but anything have no change.
>>
>
> You're adding moieties that don't exist in the force field, unless you
> have parameters from some external source (e.g. something published or
> otherwise available in a force field repository).
>
> -Justin
>
> --
> 

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Hello Mark,
This is the response I'm getting 
Please send your problem to gmx user forum 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your problem 
seems come from Gromacs cmake command parsing. The related source code is 
pretty convoluted.  Relevant Gromacs developer may answer your question.
Irina

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Thursday, February 11, 2016 11:47 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
sure the have/will on Mira too! Ask them.

Mark

On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:

> Quick clarifying question, are you sure you have the development version
> of the libxml2 package (the source with the headers and everything)?
>
> Also this might be a good time to complain to your sys-admin to install
> the libxml2-dev library, as it is used in a lot of other programs too, and
> you would just be saving everyone a headache.
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> Kosheleva 
> Sent: Thursday, February 11, 2016 12:08 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
>
> Dear gmx-users.
> I would like to install gromacs-5.1.1 on a cluster where I have only user
> privileges. The machine has arch linux-rhel_6-ppc64.
> I would like to install it with unittest support thus I need libxml2.a
> compiled library.
> The cluster does not have this library installed so I have downloaded
> libxml2-2.9.2 and compiled it with zlib support:
>  ./configure --prefix=/home/ikosh/programs/autotools-bin
> --with-python-install-dir=/home/ikosh/programs/autotools-bin
> --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
>
> Now, I would like to use this static libxml2.a library to compile
> gromacs-5.1.1:
> cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
>
> --output  just the error:
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> CMake Warning at CMakeLists.txt:543 (message):
>   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
>   recommended, because the unit-tests help to verify that GROMACS functions
>   correctly.  Most likely you are missing the libxml2-dev(el) package.
> After
>   you installed it, set GMX_BUILD_UNITTESTS=ON.
>
> Looking at the CMakeError.log in CMakeFiles:
> /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpenW':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> `gzopen64'
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> `gzdopen'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `__xmlParserInputBufferCreateFilename':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to
> `gzdirect'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlFreeZMemBuff':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to
> `deflateEnd'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpen_real':
> 

Re: [gmx-users] PMF of a single water molecule respect to a surface

[Justin Lemkul]

On 2/12/16 8:47 AM, Alexander Alexander wrote:

Dear Gromacs user,

I am calculation the PMF of a single water molecule to pull it away from
top of metallic surface along vacuum in the Z direction ,following the
Justin umbrella tutorial. I am only  interested in the behavior of PMF in
0.002 nm to 0.8 nm intervalon top of the surface, but I do not why the
population of the generated frames in this interval is really low and then
the result is so poor.

So, would you please let me know which parameter I should play around with?

I just tried 0.001 instead 0.01 as the "pull_coord1_rate" and simultaneously
3500 instead of 1000 as "pull_coord1_k", but the result got even worse.



How often are you saving the snapshots?  I presume you're referring to the 
generation of initial coordinates as references for the individual windows. If 
you don't save frequently enough, you may miss one that you need, although it 
should be pretty easy to capture something "close enough" to start.


Your biggest problem is the very short distance you're considering here.  0.002 
nm?  You're going to have massive repulsion at that distance, such that you're 
not likely to observe any stable configurations there.  Probably anything less 
than 0.1 or 0.2 nm is going to be pretty unstable, depending on the nature of 
the interactions.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Prodrg disturbed hybridization state of doubly bonded nitrogen

[Saman Yousuf ali]

Dear all,I am a beginner here. I have prepared my ligand topology file using 
prodrg, it gave me the following error,
PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set 
'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG> WARNING: deleted 
hydrogen(s) from your input.PRODRG> Molecule complexity index: 2.11.PRODRG> 
WARNING: applied 1 unusual hybridisation fixup(s).PRODRG> 13 hydrogen(s) 
added.PRODRG> Using charge groups.PRODRG> Net charge on molecule: 0.000PRODRG> 
19 partial charges 1 ambiguousPRODRG> 33 bonds 10 ambiguousPRODRG> 55 bond 
angles 34 ambiguousPRODRG> 17 improper dihedrals 2 ambiguousPRODRG> 11 
dihedrals 5 ambiguousPRODRG> Writing GROMACS topology.PRODRG> GROMACS topology 
quality on 0-10 scale: 5.8PRODRG> Keeping old coordinates.PRODRG> RMSD from 
GROMOS bond ideality (Angstrom) : 0.060PRODRG> RMSD from GROMOS angle ideality 
(degrees) : 5.631PRODRG> RMSD from GROMOS plane ideality (degrees) : 
2.317PRODRG> Number of improper improper dihedrals : 0PRODRG> Writing: 
SCRTHOWMMPGPRODRG> Normal program end.
Prodrg disturbed hybridization state of doubly bonded nitrogen atom and it 
remove double bond and attach hydrogen on this atom. Kindly suggest me how can 
I fix this problem.
Thank you.
 Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.

Contact No:
Office (92-21) 11192 (Ext 309)
Email ID: saman.yousufal...@yahoo.com
 saman@iccs.edu

   |

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Re: [gmx-users] Installation problem

[Nikhil Maroli]

Hi,
What is your system details?Do you have GPU ,if yes CUDA library is 
installed?
if not please install CUDA library and MPI packages too!
hope it will fix

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[gmx-users] DSSP secondary structure

[mohammad r]

Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein 
during the simulation but the resolution of the resulted .xpm file is very low. 
how can I increase its resolution?
Thank you, Mohammad.
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Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Mark Abraham]

Hi,

What command did you use to use their libxml2? Things work for me, but that
doesn't mean there isn't a problem :-)

Mark

On Fri, 12 Feb 2016 20:41 Irina Kosheleva 
wrote:

> Hello Mark,
> This is the response I'm getting
> Please send your problem to gmx user forum
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your
> problem seems come from Gromacs cmake command parsing. The related source
> code is pretty convoluted.  Relevant Gromacs developer may answer your
> question.
> Irina
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Thursday, February 11, 2016 11:47 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> Hi,
>
> IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
> sure the have/will on Mira too! Ask them.
>
> Mark
>
> On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:
>
> > Quick clarifying question, are you sure you have the development version
> > of the libxml2 package (the source with the headers and everything)?
> >
> > Also this might be a good time to complain to your sys-admin to install
> > the libxml2-dev library, as it is used in a lot of other programs too,
> and
> > you would just be saving everyone a headache.
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> > Kosheleva 
> > Sent: Thursday, February 11, 2016 12:08 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
> >
> > Dear gmx-users.
> > I would like to install gromacs-5.1.1 on a cluster where I have only user
> > privileges. The machine has arch linux-rhel_6-ppc64.
> > I would like to install it with unittest support thus I need libxml2.a
> > compiled library.
> > The cluster does not have this library installed so I have downloaded
> > libxml2-2.9.2 and compiled it with zlib support:
> >  ./configure --prefix=/home/ikosh/programs/autotools-bin
> > --with-python-install-dir=/home/ikosh/programs/autotools-bin
> > --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
> >
> > Now, I would like to use this static libxml2.a library to compile
> > gromacs-5.1.1:
> > cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> > -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> > -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> > -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> >
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> >
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> >
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> > -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> > -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> > -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> > -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
> >
> > --output  just the error:
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> > CMake Warning at CMakeLists.txt:543 (message):
> >   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
> >   recommended, because the unit-tests help to verify that GROMACS
> functions
> >   correctly.  Most likely you are missing the libxml2-dev(el) package.
> > After
> >   you installed it, set GMX_BUILD_UNITTESTS=ON.
> >
> > Looking at the CMakeError.log in CMakeFiles:
> > /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> > CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> > /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> > -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> > 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> > -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> > CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> > s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > `xmlGzfileOpenW':
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> > `gzopen64'
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> > `gzdopen'
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > 

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Hi,
I have compiled my own libxlm2-2.9.3 (this is not a devel from what I know)
Using:
./configure CC=mpixlcxx_r --prefix=/home/ikosh/programs/autotools-bin 
--with-python-install-dir=/home/ikosh/programs/autotools-bin --with
-zlib=/soft/libraries/alcf/current/xl/ZLIB --enable-static --disable-shared
This did not produce errors in config.log

Cmake:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/home/ikosh/programs/autotools-bin/include 
-DFFTWF_LIBRARY=/home/ikosh/programs/autotools-bin/lib/libfftw3f.a 
-DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  
-DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a 
-DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include 
-DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

The compiler flags are static. There is no static libxml2.a installed on vesta 
as far as I know, however there are dynamic libxml2.so libraries which I did 
not use because CMAKE_TOOLCHAIN_FILE is static and I use all flags for static 
libraries.
Does  this approach pose a problem?
I am really interested in the way you have used libxml2 for the compilation on 
vesta.
Irina.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Friday, February 12, 2016 3:47 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

What command did you use to use their libxml2? Things work for me, but that
doesn't mean there isn't a problem :-)

Mark

On Fri, 12 Feb 2016 20:41 Irina Kosheleva 
wrote:

> Hello Mark,
> This is the response I'm getting
> Please send your problem to gmx user forum
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your
> problem seems come from Gromacs cmake command parsing. The related source
> code is pretty convoluted.  Relevant Gromacs developer may answer your
> question.
> Irina
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Thursday, February 11, 2016 11:47 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> Hi,
>
> IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
> sure the have/will on Mira too! Ask them.
>
> Mark
>
> On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:
>
> > Quick clarifying question, are you sure you have the development version
> > of the libxml2 package (the source with the headers and everything)?
> >
> > Also this might be a good time to complain to your sys-admin to install
> > the libxml2-dev library, as it is used in a lot of other programs too,
> and
> > you would just be saving everyone a headache.
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> > Kosheleva 
> > Sent: Thursday, February 11, 2016 12:08 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
> >
> > Dear gmx-users.
> > I would like to install gromacs-5.1.1 on a cluster where I have only user
> > privileges. The machine has arch linux-rhel_6-ppc64.
> > I would like to install it with unittest support thus I need libxml2.a
> > compiled library.
> > The cluster does not have this library installed so I have downloaded
> > libxml2-2.9.2 and compiled it with zlib support:
> >  ./configure --prefix=/home/ikosh/programs/autotools-bin
> > --with-python-install-dir=/home/ikosh/programs/autotools-bin
> > --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
> >
> > Now, I would like to use this static libxml2.a library to compile
> > gromacs-5.1.1:
> > cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> > -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> > -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> > -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> >
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> >
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> >
>