[gmx-users] Pressure from Ke and Virial from .edr

[Hardy, Adam]

Dear All,

As part of my work I need to recalculate the pressure from the kinetic energy 
and virial.

I start with the equation (2/V)(Ke – Vir).

The units given for the virial and kinetic energy (as taken from the .edr file) 
are given in kJ/mol so when I calculate the values of the pressure components 
and convert units I’m left with a pressure in Bar/mol (kJ/m^3 mol -> 10^3 
Pa/mol -> 10^-2 Bar/mol). My initial thought was to multiply by Avogadro’s 
number but this gives me a number that is~750 times too large so clearly I’m 
missing something. Where am I going wrong?

Many thanks,

Adam


--
Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot Watt University
Edinburgh, EH14 4AS
Phone: +441314513074
ah...@hw.ac.uk
--


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Re: [gmx-users] Running ultiple job in core?

[Hardy, Adam]

If you only have the one GPU, then both simulations will be trying to share the 
GPU resource, so they will not be able to obtain the same performance compared 
to running them separately. 

The only true solution is to use a second GPU. You may or may not find it 
useful to run one of your simulations with the GPU and one without, you can 
force a simulation to run CPU only by using: -nb CPU.

Adam

> On 19 Nov 2015, at 02:45, RJ  wrote:
> 
> Hi there,
> 
> 
> I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two 
> simulation job by assigning 12 threads for each job. I have tried using 
> "-ntomp 12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt 
> get the similar speed as if run them alone with 12 threads. I have even used 
> "-pin on" but haven't get any significant changes in the speed?
> 
> 
> Its much appreciated if you could provide the hints on it. Thanks a lot.
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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

[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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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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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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\
>&

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

[Hardy, Adam]

Just to follow up on this, upgrading cmake from 2.8.8 (to 3.13 in this case) 
solved the problem.

Adam


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Irina 
Kosheleva 
Sent: 12 February 2016 15:18
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

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] Box Vectors in .gro file

[Hardy, Adam]

Dear all,

I'm trying to set up a simulation which uses a parallelepiped box. The trouble 
I'm having is I don't quite understand the notation used to describe it in the 
.gro file.

I have read the detail here: http://manual.gromacs.org/current/online/gro.html 
but it's not quite enough for me.

I am sure it's some sort of standard notation but I've not come across before 
and every time I go searching for "box vectors" or similar I just get a lot of 
pages about cardboard vector art.

Could someone give an explanation or point me to somewhere I can learn about 
this?

Thanks,

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK

- 
We invite research leaders and ambitious early career researchers to 
join us in leading and driving research in key inter-disciplinary themes. 
Please see www.hw.ac.uk/researchleaders for further information and how
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[gmx-users] Lithium Ions in Gromos53A6

[Hardy, Adam]

Dear All,

I find myself requiring lithium ions in a simulation using (a variant of) the 
Gromos53A6 forcefield.

Chaging forcefields is not an appealing proposition due to the time already 
invested in the current one, so I was wondering had any suggestions or has 
perhaps gone to the effort of creating parameters for it?

Thanks,

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


- 
We invite research leaders and ambitious early career researchers to 
join us in leading and driving research in key inter-disciplinary themes. 
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.

Heriot-Watt University is a Scottish charity
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[gmx-users] Option to run mdrun without GPUs

[Hardy, Adam]

Dear Gromacs Users,

I have a version of Gromacs 5 installed with GPU support. With the setup of my 
system I would find it useful to occasaionaly run simulations without either of 
the GPUs, is there an easy way to do this (such as a flag to pass to mdrun) as 
I can't find one? Otherwise do I just need to compile a seperate executable 
without GPU support?

Thanks,


Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


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[gmx-users] Virial Calculation in Gromacs Source Code

[Hardy, Adam]

Dear All,

As part of my work I am looking at making modifications to calculation of the 
virial in gromacs. I have spent some time making myself a bit familiar with the 
gromacs source and I've looked at the doxygen generated docs and through the 
various pages on the developer section of the website but I'm still at a bit of 
a loss as to where to start making these modifications. I've found a calc_vir.c 
source file and tried to follow the backwards and I also see references to the 
virial in do_md and global_stat but I'm struggling to put it all together.

Are there any more sources of information about the source code that I haven't 
found or can anyone point me to where I need to be looking to make changes to 
the virial calculation?

Thanks in advance,

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


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Re: [gmx-users] Pressure coupling error

[Hardy, Adam]

You also need to add a second value for compressibility as you have done for 
tau-p and ref-p.

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Riccardo Concu 
[ric.co...@gmail.com]
Sent: 13 January 2015 15:28
To: gmx-us...@gromacs.org
Subject: [gmx-users] Pressure coupling error

Hi all,
I’m receiving this error from grompp:

ERROR 1 [file npt.mdp, line 50]:
  Pressure coupling not enough values (I need 2)

I think I’ve inserted in the .mdo the required values:
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5000;100ns
comm-mode= Linear
nstcomm  = 10
comm-grps= System
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 80
nstxtcout= 750
xtc-precision= 1500
xtc-grps = System
energygrps   =  WAT MET HEX
nstlist  = 20
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
rlist= 1.1
coulombtype  = PME
rcoulomb = 1.1
;cutoff-scheme = Verlet
vdw-type = Cut-off
rvdw = 1.5
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 6
ewald_rtol   = 1e-5
optimize_fft = yes
Tcoupl   = Nose-hoover
tc-grps  = WAT MET HEX
tau_t=  0.1 0.1 0.1
ref_t=  298 298 298
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
tau_p= 1.0  1.0
ref_p  = 1.0  1.0
compressibility  = 4.5e-5
gen_vel  = no
gen_temp = 298
gen_seed = 173529
constraints  = all-bonds
constraint-algorithm = Lincs
lincs-order  = 4
lincs-iter   = 1
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Re: [gmx-users] GMX_THREAD_MPI=ON" does not exis

[Hardy, Adam]

You seem to be missing a -D infront of the thread mpi option.

On 29 Nov 2013 16:54, Mahboobeh Eslami  wrote:
hi my friends, please help me

i use following command for install gromacs:

CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. 
-DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF 
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON 
-DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs
 but i get following error:

CMake Error: The source directory 
"/home/elahe/.local/share/Trash/files/gromacs-4.2.6.3/build/GMX_THREAD_MPI=ON" 
does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
thanks
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Re: [gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.

[Hardy, Adam]

As far as I understand, if you have configured it correctly with that version, 
it will use all available cores unless you specify otherwise. The precise 
command for this escapes me for the moment but it is documented on the gromacs 
website. When you run mdrun it will tell you how many threads it is using.

On 29 Nov 2013 20:17, Mahboobeh Eslami  wrote:
i want to install gromacs4.6.3 on 8 core.
i use following command:

CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. 
-DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF 
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON 
-DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs
is it correct?
What command do I use to use 8 cores? which valid command line argument do i 
use by mdrun_mpi_d for 8 cores.
thanks a lot
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Re: [gmx-users] Atomistic Simulation

[Hardy, Adam]

I've just started doing atomistic simulations over the last few weeks as well 
and can share what I've learned so far.

I have been using 'automated topology builder'. It only uses the gromos 53a6 
forcefield so eliminates the choice if you want to use it. ATB generates the 
pdb and itp files for you. There are a lot of molecules already on there or you 
can submit you're own using a java script molecule builder.

There may well be other ways to do this but I haven't found them yet.

On 3 Dec 2013 10:14, panzu  wrote:
  Hello to everybody,

I am new in atomistic simulations and a have some doubts about how to do it.

I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
My  questions are, ¿Where do I get the pdb files of these molecules
from? and ¿How do I know which force field I should choose in pdb2gmx
in order to make the itp file?

Thanks in advance,

Panzu



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Re: [gmx-users] Atomistic Simulation

[Hardy, Adam]

You don't need to. Gromacs accepts pdb, gro and several other coordinate file 
formats.

On 4 Dec 2013 14:30, panzu  wrote:

so How do I convert from .pdb to .gro?

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[gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

[Hardy, Adam]

Dear All,

I am attempting to make modifications to the Gromos 53A6 forcefield in order to 
implement the Gromos 56Acarbo forcefield in GROMACS. Most of the modifications 
are straightforward except for some of the LJ parameters. As well as simple 
adjustments to most of the 1-4 interaction parameters there is a requirement to 
implement a) some 1-4 interaction parameters when the 2 and 3 atoms are 
specific combinations and b) some 1-5 special parameters.

As I'm fairly new to GROMACS I was hoping someone could verify my method and 
clarify one or two things.

I would need to set nrexcl to 4 in order to stop the special 1-5 parameters 
being calculated twice (once "normal" LJ, one "special").

In the itp file I would then need to explicitly provide all the special 1-4 and 
all the 1-5 LJ parameters (in addition to listing the normal 1-4 interaction 
pairs) as GROMACS cannot look these up in the forcefield files.

If gen-pairs is set to yes, does it overwrite parameters given in the itp file? 
This way I would not have to go through and explicitly list the "normal" 1-4 
interaction parameters in the itp file.

I hope that is clear.

Many thanks in advance,

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


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Re: [gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

[Hardy, Adam]

Bogdan, I had found that a little while ago but was unable to find again so 
thankyou for pointing me to it again and writing it in the first place.

Jon, I hadn't found those file previously and they are consistent with what I 
have come up with independently so I guess that is a good sign. Out of interest 
do you use GLYCAM with GROMACS? It's something I have wanted to try but 
couldn't see a way to implement the different LJ scaling factors into GROMACS 
that seem to be required for systems with both carbohydrate and 
non-carbohydrate molecules.

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jon Kapla 
[jon.ka...@mmk.su.se]
Sent: 12 May 2014 12:45
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

Hi,

There have been some efforts of trying to implement the 56Acarbo before,
and there are some files that you might want to take a look at in the
user contributions section on the Gromacs website. I think the files
there only delas with 1-4 glycosidic linkages, but I guess it should be
straightforward to extend it to other connections using the dihedral
types from the 56Acarbo paper. Anyway the files might come in handy for
you if you haven't dicovered them yet. I can't say anything about the
quality of the conversion though, since I haven't used those parameters
myself, but it seems they use the same approach as you do (and as I did
a couple of years ago trying to accomplish the same thing, but I swiched
to Glycam parameters before I finished the project). I guess the best
thing would be to try to get hold of single point energies from gromos
and compare them with your conversion.

http://www.gromacs.org/Downloads/User_contributions/Force_fields

Regards
Jon Kapla


On 2014-05-12 12:49, Hardy, Adam wrote:
> Dear All,
>
> I am attempting to make modifications to the Gromos 53A6 forcefield in order 
> to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the 
> modifications are straightforward except for some of the LJ parameters. As 
> well as simple adjustments to most of the 1-4 interaction parameters there is 
> a requirement to implement a) some 1-4 interaction parameters when the 2 and 
> 3 atoms are specific combinations and b) some 1-5 special parameters.
>
> As I'm fairly new to GROMACS I was hoping someone could verify my method and 
> clarify one or two things.
>
> I would need to set nrexcl to 4 in order to stop the special 1-5 parameters 
> being calculated twice (once "normal" LJ, one "special").
>
> In the itp file I would then need to explicitly provide all the special 1-4 
> and all the 1-5 LJ parameters (in addition to listing the normal 1-4 
> interaction pairs) as GROMACS cannot look these up in the forcefield files.
>
> If gen-pairs is set to yes, does it overwrite parameters given in the itp 
> file? This way I would not have to go through and explicitly list the 
> "normal" 1-4 interaction parameters in the itp file.
>
> I hope that is clear.
>
> Many thanks in advance,
>
> Adam Hardy
> PhD Student
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS, UK
>
>
> -
> Sunday Times Scottish University of the Year 2011-2013
> Top in the UK for student experience
> Fourth university in the UK and top in Scotland (National Student Survey 2012)
>
> We invite research leaders and ambitious early career researchers to
> join us in leading and driving research in key inter-disciplinary themes.
> Please see www.hw.ac.uk/researchleaders for further information and how
> to apply.
>
> Heriot-Watt University is a Scottish charity
> registered under charity number SC000278.
>
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