Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Mark Abraham]

Hi,

On Thu, Oct 22, 2015 at 6:58 PM Ana Marija 
wrote:

> I just tried to install it with:
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF
>
> but the error is the same as above.
>

It can't be if you've done it properly. Use a new, empty build directory.


> My goal with this installation (without cross compiler) was to use it to
> generate input files and than use another installation of gromacs compiled
> with cross compilers to complete the run. Where I would use the same
> version of gromacs  in both cases, 4.6.7. Can you please confirm me that
> this is acceptable approach?
>

Yes, but needlessly complex. You can run grompp anywhere, copy the file to
the Cray, and use the resulting .tpr on the compute nodes, like I said a
while ago.


> The reason why I can't use newer version of gromacs is that I only have
> cmake 2.8.4 on this machine and it is impossible to install newer version
> of cmake because it is tied to gnu version we got from Cray etc.
>

Perhaps Cray supplied a cmake, but it doesn't run on the compute nodes, and
has nothing at all to do with the back end compilers, and your system
admins can and should be willing to download and install a more recent
cmake for you and everybody else :-)

Mark


> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll 
> wrote:
>
>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija 
>> wrote:
>>
>>> I installed it via:
>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>
>>> then I was running it on login nodes via:
>>>
>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>>
>>>
>>> but I didn't get .tpr file, and output was this:
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>>> Generated 1081 of the 1081 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 994 of the 1081 1-4 parameter combinations
>>>
>>> ---
>>> Program grompp, VERSION 4.6.7
>>> Source code file:
>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>>
>>> Fatal error:
>>> [ file tip3p.itp, line 39 ]:
>>> Atom index (1) in settles out of bounds (1-0).
>>> This probably means that you have inserted topology section "settles"
>>> in a part belonging to a different molecule than you intended to.
>>> In that case move the "settles" section to the right molecule.
>>>
>>> can you please advise what should I do in this situation?
>>>
>>
>> As Justin said, this isn't an issue with the GROMACS build anymore (but
>> rather with the inputs). So it seems that the original problem is solved -
>> unless you really need to run grompp on the compute nodes.
>>
>> BTW, I hope you know that 4.6.7 is a rather old and outdated version; the
>> 5.0 and 5.1 series has been released since and the former is AFAIK
>> supported by PLUMED!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>>>
>>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
>>> sokovic.anamar...@gmail.com> wrote:
>>>
 so is it ok to try this?
 cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
 -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
 -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
 -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
 -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
 -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON



 On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
 mark.j.abra...@gmail.com> wrote:

> Hi,
>
> Your blas and lapack were compiled with gfortran, but in a way that
> they require that one links further dependencies to use them later on. So
> compile them better, or use dynamic linking.
>
> But 99.9% of GROMACS users do not need to get involved with this, so
> just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use 
> its
> internal versions.
>
> Mark
>
>

>>>
>>
>
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[gmx-users] MD of two structure together-receptor+ligand

[Nikhil Maroli]

Dear Gromacs users,
i wanted to do MD after docking,i done docking and i selected one
conformation  i have receptor pdb and ligand pdb and i made one pdb with
both ?
now i wanted to do MD and see how the interaction goes on and to
learn/predict inhibition and antagonist behavior of the system.
so can anyone tell me how should start ?
should i start with one single pdb if yes how should i add topolgy for
drugs?
i have topolgy parameters from individual system generated from the server
i hope someone can help out here.
Thanks in advance

-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Ebert Maximilian]

Thanks for the answer. I was checking the CHARMM22 All-Hydrogen Parameter File 
for Proteins par_all22_prot.inp and the section non-bonded:

nitrogens
N  0.00  -0.20 1.85   0.00  -0.000100 1.85 ! 
ALLOW   PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC20.00  -0.20 1.85 ! ALLOW   POL
! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH10.00  -0.20 1.85   0.00  -0.20 1.55 ! 
ALLOW   PEP POL ARO
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH20.00  -0.20 1.85 ! ALLOW   POL
! adm jr.
NH30.00  -0.20 1.85 ! ALLOW   POL
! adm jr.
NP 0.00  -0.20 1.85 ! ALLOW  PRO
! N-terminal proline; from 6-31g* +ProNH2  RLD 9/28/90
NPH0.00  -0.20 1.85 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR10.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NR20.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NR30.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NY 0.00  -0.20 1.85 ! ALLOW   ARO
! trp, JWK

All nitrogen have the same LJ parameter. I haven’t checked CGenFF but I will 
definitely look into that. Thanks for you comment.

Max

> On Oct 22, 2015, at 12:40 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 10/22/15 11:04 AM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I already asked the question in the AMBER list but couldn’t get an answer. 
>> So I try my luck here even though it is a bit off topic in the GROMACS list. 
>> I was wondering why the different atom types of H, C and O have different 
>> LJ-parameter but for all the different types of N we see the identical 
>> parameters in OPLS, AMBER and CHARMM?
>> 
> 
> Sometimes that's just the way force fields work out.  Electrostatics are 
> tuned first, and then condensed phase interactions are targeted for LJ 
> refinement. Given the nature of most N interactions (either lone pair or via 
> polar/hydrogen bonding interactions with an H), the electrostatics generally 
> dominate, so a generic LJ parameter that is common to different moieties is 
> sufficient.
> 
> In CGenFF, there are several N types with different LJ, though the 
> biomolecular parts of the CHARMM force field share the same parameters.
> 
> -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] energy minimization error

[faride badalkhani]

Hi,

I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
But, every time the system blows up at energy minimization step. Therefore,
according to what Mark had recommended I decided to start with a much
smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:

https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0

Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance
Farideh
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Re: [gmx-users] energy minimization error

[Mark Abraham]

Hi,

Did you inspect your topology like I suggested? You need to know that there
are bonds exactly where you intend them, before doing any calculations with
them.

Mark

On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani 
wrote:

> Hi,
>
> I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> But, every time the system blows up at energy minimization step. Therefore,
> according to what Mark had recommended I decided to start with a much
> smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> optimized it at M062x/6-31G* level, before starting the MD simulations.
> Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> residue by residue. After that, I started simulation procedure and
> continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> errors in energy minimization step, and the potential energy - EM step plot
> was reasonable. But, when I loaded em.gro file in VMD, the structure was
> completely messed up as in G3 dendrimer. This time I continued the MD
> simulation until production MD, and there was no error. However, the system
> is blown up. You can access all the simulation files, pdb structure, and
> the photos of G1 structure before and after EM step via:
>
> https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
>
> Since I am a beginner in this area, I do not know what is the solution for
> this problem.
> Do you think errors that occur during the G3 simulation are relevant to the
> initial structure?
> any suggestion or recommendation is appreciated.
>
> Thanks in advance
> Farideh
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Re: [gmx-users] walp lipids around protein in membrane protein simulation

[Mark Abraham]

Hi,

If the protein has rotated with respect to the bilayer over time, then you
cannot rotate a simulation frame to align simultaneously the bilayer with
the bilayer and the protein with the protein.

Mark

On Thu, Oct 22, 2015 at 8:58 AM 凌未风  wrote:

> Hi All:
>
> I am running a membrane protein simulation, in which the protein is
> inserted into a membrane bilayer.
>  During my simulations, the protein rotate and diffuse on the bilayer
> plane. I am trying to put the protein in the center of the bilayer and
> align the protein with the initial conformation.
> I did the  following things to put the protein in the center of the
> bilayer:  trjconv -s *.tpr -f *.xtc -center -pbc whole -o *.xtc
> However,  when I tried to align the protein with the initial
> conformation by the  following command:  trjconv -s *.tpr -f *.xtc -fit
> rot+trans -o *.xtc
>  In the output trajectory, the protein is at the center of the
> bilayer  and aligned with the initial conformation, but the x and y axis of
> the  bilayer is not consistent with the initial conformation, i.e., the
> bilayer rotated on the xy plane.
> I understand this is because I aligned the protein to the initial
> conformation.
>  My question is: is there any way to  put the protein at the center
> of  bilayer and align the protein to the initial conformation while still
> keep the x and y axes of the bilayer consistent with the initial  structure?
> Thanks very much. I really appreciate for any help.
> With my best regards,
> Ruo-Xu Gu
> University of Calgary
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

Thanks everybody for all your help!

On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija 
> wrote:
>
>> I just tried to install it with:
>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>> -DGMX_GPU=OFF -DGMX_MPI=OFF
>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>> -DGMX_X11=OFF
>>
>> but the error is the same as above.
>>
>
> It can't be if you've done it properly. Use a new, empty build directory.
>
>
>> My goal with this installation (without cross compiler) was to use it to
>> generate input files and than use another installation of gromacs compiled
>> with cross compilers to complete the run. Where I would use the same
>> version of gromacs  in both cases, 4.6.7. Can you please confirm me that
>> this is acceptable approach?
>>
>
> Yes, but needlessly complex. You can run grompp anywhere, copy the file to
> the Cray, and use the resulting .tpr on the compute nodes, like I said a
> while ago.
>
>
>> The reason why I can't use newer version of gromacs is that I only have
>> cmake 2.8.4 on this machine and it is impossible to install newer version
>> of cmake because it is tied to gnu version we got from Cray etc.
>>
>
> Perhaps Cray supplied a cmake, but it doesn't run on the compute nodes,
> and has nothing at all to do with the back end compilers, and your system
> admins can and should be willing to download and install a more recent
> cmake for you and everybody else :-)
>
> Mark
>
>
>> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll 
>> wrote:
>>
>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija >> > wrote:
>>>
 I installed it via:
 cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
 -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
 -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
 -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
 -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
 -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON

 then I was running it on login nodes via:

 /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
 /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
 /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
 /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
 /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr


 but I didn't get .tpr file, and output was this:
 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
 Generated 1081 of the 1081 non-bonded parameter combinations
 Generating 1-4 interactions: fudge = 0.5
 Generated 994 of the 1081 1-4 parameter combinations

 ---
 Program grompp, VERSION 4.6.7
 Source code file:
 /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803

 Fatal error:
 [ file tip3p.itp, line 39 ]:
 Atom index (1) in settles out of bounds (1-0).
 This probably means that you have inserted topology section "settles"
 in a part belonging to a different molecule than you intended to.
 In that case move the "settles" section to the right molecule.

 can you please advise what should I do in this situation?

>>>
>>> As Justin said, this isn't an issue with the GROMACS build anymore (but
>>> rather with the inputs). So it seems that the original problem is solved -
>>> unless you really need to run grompp on the compute nodes.
>>>
>>> BTW, I hope you know that 4.6.7 is a rather old and outdated version;
>>> the 5.0 and 5.1 series has been released since and the former is AFAIK
>>> supported by PLUMED!
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>>
>>>

 On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
 sokovic.anamar...@gmail.com> wrote:

> so is it ok to try this?
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
> mark.j.abra...@gmail.com> wrote:
>
>> Hi,
>>
>> Your blas and lapack were compiled with gfortran, but in a way that
>> they require that one links further dependencies to use them later on. So
>> compile them better, or use dynamic linking.
>>
>> But 99.9% of GROMACS users do not need to get involved with this, so
>> just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and 

Re: [gmx-users] MD of two structure together-receptor+ligand

[Justin Lemkul]

On 10/22/15 1:23 PM, Nikhil Maroli wrote:

Dear Gromacs users,
i wanted to do MD after docking,i done docking and i selected one
conformation  i have receptor pdb and ligand pdb and i made one pdb with
both ?
now i wanted to do MD and see how the interaction goes on and to
learn/predict inhibition and antagonist behavior of the system.
so can anyone tell me how should start ?
should i start with one single pdb if yes how should i add topolgy for
drugs?
i have topolgy parameters from individual system generated from the server
i hope someone can help out here.


Google knows a lot, too.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-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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Re: [gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation

[Tomek Wlodarski]

Dear Mark,

Thank you for suggestion.
I run plain mdrun to advance each simulation to the same time point and use
new cpt to restart replica exchange simulations.
It started without any error from the proper time point and metadynamics
was running OK.
However, when it finished it did not write any new cpt files... so when I
restarted it again it started from the the same time point like the one
before
Any idea what may cause this problem?
Thank you.
Best,

tomek

On Tue, Oct 13, 2015 at 11:43 AM, Mark Abraham 
wrote:

> Hi,
>
> Unfortunately, that should
> a) never happen,
> b) given a), rarely happen identically for successive checkpoints,
> c) is even more strange if your time step is a normal ~2fs, and
> d) is not easy to fix.
>
> To address a-c), it would be good for you to get some feedback from the
> PLUMED developers about whether others have reported such problems.
> Offhand, I don't know of any plain GROMACS user who's been able to produce
> such checkpoint files. Last time I looked at their code I didn't see
> anything that could do this, but that was 1.x. It is also conceivable that
> this is a bug in your MPI layer.
>
> For d), you can try
> * back up your files
> * use plain mdrun to advance all of the 194440.010 files by one step (e.g.
> gmx mdrun -nsteps 1 -s old -cpi state)
> * same for the 194440.002 files by as many steps as you need to catch up to
> the others
> * restart mdrun -multi -replex
>
> Simulations have an internal part number that is expected to match, which
> is why you can't just run an extra part to catch up the simulations that
> are lagging.
>
> Mark
>
> On Tue, Oct 13, 2015 at 12:05 PM Tomek Wlodarski <
> tomek.wlodar...@gmail.com>
> wrote:
>
> > Dear GROMACS users,
> >
> > I am running REMD simulation with Gromacs 5.0.4 and PLUMED 2.1 for
> already
> > around 200ns with many smooth restarts. Unfortunately now something went
> > wrong because I got error that:
> >
> > The 6 subsystems are not compatible
> >
> > So I checked with gmxcheck cpt files
> > replica 1: Last frame -1 time 194440.010
> > replica 2: Last frame -1 time 194440.010
> > replica 3: Last frame -1 time 194440.010
> > replica 4: Last frame -1 time *194440.002*
> > replica 5: Last frame -1 time 194440.010
> > replica 6: Last frame -1 time *194440.002*
> > Same situation is in _prev.cpt
> > replica 1: Last frame -1 time 194400.010
> > replica 2: Last frame -1 time 194400.010
> > replica 3: Last frame -1 time 194400.010
> > replica 4: Last frame -1 time *194400.002*
> > replica 5: Last frame -1 time 194400.010
> > replica 6: Last frame -1 time *194400.002*
> >
> > Any idea how to restart simulation when both cpt and _prev.cpt file seem
> to
> > be broken?
> > Why this happened and how to prevent it?
> > Thank you.
> > All the best,
> >
> > tomek
> > --
> > 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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[gmx-users] suspension of colloids in GROMACS

[CARDELLINI ANNALISA]

Dear gromacs users,
In one project, I have to do some coarse grained molecular 
dynamics (CGMD) simulations of nano-colloids (inorganic 
particles 100-150 nm, 3%wt max very dilute) by using soft 
potentials (e.g. DLVO) and implicit solvent (Brownian 
dynamics or fluctuating hydrodynamics).
 
1) I am wondering if GROMACS is the right tool for that... 
I mean, in principle, it should be possible but is there 
explicit support for colloidal simulations? How can we 
introduced a proper force field for particles 
interactions?


2) Do you know someone in the GROMACS team doing colloidal 
simulations? Anyone else in the World?
 
Your help would be highly appreciated.
 
Best regards,

Annalisa




Annalisa Cardellini, M.Sc.
Ph.D. student

E-mail: annalisa.cardell...@polito.it
SMaLL: http://www.polito.it/small
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Barnett, James W]

On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
> Hi,
> 
> I installed gromacs 4.6.7 with plumed like this:
> module swap PrgEnv-cray PrgEnv-gnu
> module load fftw/3.3.4.0
> module load cray-mpich/7.0.5
> module load gsl/1.15
> module load cmake
> #in /lustre/beagle2/ams/new/gromacs make directory lib2
> 
> mkdir lib2
> 
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> 
> tar zxvf plumed-2.2.0.tgz
> cd plumed-2.2.0
> 
> ./configure CC=cc CXX=CC F77=ftn
> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> --disable-basic-warnings --disable-openmp
> 
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> CC=cc
> FC=gfortran
> LDF90=gfortran
> CFLAGS=-g -O2
> CXX=CC
> CXXFLAGS=-O -fPIC
> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> LDFLAGS=
> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> ###
> 
> make
> make install
> 
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> 
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/new/modulefiles/)
> #2. Copy file: cp
> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> #4. type "module load plumed/2.2.0"
> 
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> module use /lustre/beagle2/ams/new/modulefiles/
> module load plumed/2.2.0
> 
> ### instal gromacs 4.6.7
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> tar zxvf gromacs-4.6.7.tar.gz
> cd gromacs-4.6.7/
> ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
> 
> 
> PLUMED patching tool
> 
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2
> 
> Choose the best matching code/version:3
> 
> mkdir build
> cd build
> 
> 
> export BUILD_WITH_INSTALL_RPATH=TRUE
> export INSTALL_RPATH=""
> export SKIP_BUILD_RPATH=TRUE
> export
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
> 
> #in /lustre/beagle2/ams/new/gromacs make directory lib
> 
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> 
> 
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default
> /lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/li
> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau
> lt/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos
> /lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/de
> fault/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_
> detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON
> 
> 
> make
> make install
> 
> I am getting Segmentation error if I run it like this:
> 
> #!/bin/bash
> #PBS -N test
> #PBS -j oe
> #PBS -l walltime=01:00:00
> #PBS -l mppwidth=96
> 
> source /opt/modules/default/init/bash
> 
> cd $PBS_O_WORKDIR
> module swap PrgEnv-cray PrgEnv-gnu
> export 

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

if I do that that I got: Illegal Instruction error
which makes sense because I compiled gromacs with cross compiler for
compute nodes

On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W 
wrote:

> On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
> > Hi,
> >
> > I installed gromacs 4.6.7 with plumed like this:
> > module swap PrgEnv-cray PrgEnv-gnu
> > module load fftw/3.3.4.0
> > module load cray-mpich/7.0.5
> > module load gsl/1.15
> > module load cmake
> > #in /lustre/beagle2/ams/new/gromacs make directory lib2
> >
> > mkdir lib2
> >
> > ams@login1:/lustre/beagle2/ams/lib2>ln -s
> > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > ams@login1:/lustre/beagle2/ams/lib2>ln -s
> > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> >
> > tar zxvf plumed-2.2.0.tgz
> > cd plumed-2.2.0
> >
> > ./configure CC=cc CXX=CC F77=ftn
> > LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> > --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> > --disable-basic-warnings --disable-openmp
> >
> > ###Makefile.conf should look like this, if not please delete all
> > extra stuff before proceeding to make step
> > CC=cc
> > FC=gfortran
> > LDF90=gfortran
> > CFLAGS=-g -O2
> > CXX=CC
> > CXXFLAGS=-O -fPIC
> > CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> > -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
> -DHAVE_INTTYPES_H=1
> > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> > -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> > -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> > -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> > -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> > LDFLAGS=
> > DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> > LIBS=-ldl
> > SOEXT=
> > LD=CC
> > LDSO=CC -shared
> > GCCDEP=CC
> > prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> > ###
> >
> > make
> > make install
> >
> > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> >
> > #1. Make a directory for modulefiles (e.g.
> > /lustre/beagle2/ams/new/modulefiles/)
> > #2. Copy file: cp
> > /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> > /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> > #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> > #4. type "module load plumed/2.2.0"
> >
> > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> > module use /lustre/beagle2/ams/new/modulefiles/
> > module load plumed/2.2.0
> >
> > ### instal gromacs 4.6.7
> > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> > tar zxvf gromacs-4.6.7.tar.gz
> > cd gromacs-4.6.7/
> > ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> > --static
> >
> >
> > PLUMED patching tool
> >
> > 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> > 2) gromacs-4.5.54) gromacs-5.06) namd-2.88)
> qespresso-5.0.2
> >
> > Choose the best matching code/version:3
> >
> > mkdir build
> > cd build
> >
> >
> > export BUILD_WITH_INSTALL_RPATH=TRUE
> > export INSTALL_RPATH=""
> > export SKIP_BUILD_RPATH=TRUE
> > export
> >
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
> >
> > #in /lustre/beagle2/ams/new/gromacs make directory lib
> >
> > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> >
> >
> > cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> > -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-
> > gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> > gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> >
> gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default
> >
> /lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/li
> >
> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau
> >
> lt/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos
> >
> /lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/de
> >
> fault/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_
> > detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> > -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> > -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> > -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> >
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build
> > 

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Szilárd Páll]

On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija 
wrote:

> if I do that that I got: Illegal Instruction error
> which makes sense because I compiled gromacs with cross compiler for
> compute nodes
>

just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
-DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
login node.


>
> On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W 
> wrote:
>
> > On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
> > > Hi,
> > >
> > > I installed gromacs 4.6.7 with plumed like this:
> > > module swap PrgEnv-cray PrgEnv-gnu
> > > module load fftw/3.3.4.0
> > > module load cray-mpich/7.0.5
> > > module load gsl/1.15
> > > module load cmake
> > > #in /lustre/beagle2/ams/new/gromacs make directory lib2
> > >
> > > mkdir lib2
> > >
> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s
> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s
> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> > >
> > > tar zxvf plumed-2.2.0.tgz
> > > cd plumed-2.2.0
> > >
> > > ./configure CC=cc CXX=CC F77=ftn
> > > LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> > > --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> > > --disable-basic-warnings --disable-openmp
> > >
> > > ###Makefile.conf should look like this, if not please delete
> all
> > > extra stuff before proceeding to make step
> > > CC=cc
> > > FC=gfortran
> > > LDF90=gfortran
> > > CFLAGS=-g -O2
> > > CXX=CC
> > > CXXFLAGS=-O -fPIC
> > > CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> > > -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> > > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> > > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> > > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
> > -DHAVE_INTTYPES_H=1
> > > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> > > -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> > > -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> > > -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1
> -D__PLUMED_HAS_EXECINFO=1
> > > -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> > > LDFLAGS=
> > > DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> > > LIBS=-ldl
> > > SOEXT=
> > > LD=CC
> > > LDSO=CC -shared
> > > GCCDEP=CC
> > > prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> > > ###
> > >
> > > make
> > > make install
> > >
> > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> > >
> > > #1. Make a directory for modulefiles (e.g.
> > > /lustre/beagle2/ams/new/modulefiles/)
> > > #2. Copy file: cp
> > > /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> > > /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> > > #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> > > #4. type "module load plumed/2.2.0"
> > >
> > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> > > module use /lustre/beagle2/ams/new/modulefiles/
> > > module load plumed/2.2.0
> > >
> > > ### instal gromacs 4.6.7
> > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> > > tar zxvf gromacs-4.6.7.tar.gz
> > > cd gromacs-4.6.7/
> > > ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch
> -p
> > > --static
> > >
> > >
> > > PLUMED patching tool
> > >
> > > 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> > > 2) gromacs-4.5.54) gromacs-5.06) namd-2.88)
> > qespresso-5.0.2
> > >
> > > Choose the best matching code/version:3
> > >
> > > mkdir build
> > > cd build
> > >
> > >
> > > export BUILD_WITH_INSTALL_RPATH=TRUE
> > > export INSTALL_RPATH=""
> > > export SKIP_BUILD_RPATH=TRUE
> > > export
> > >
> >
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
> > >
> > > #in /lustre/beagle2/ams/new/gromacs make directory lib
> > >
> > > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> > >
> > >
> > > cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> > > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> > > -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-
> > > gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> > > gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> > >
> >
> gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default
> > >
> >
> /lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/li
> > >
> >
> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau
> > >
> >
> lt/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos
> > >
> >
> 

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Szilárd Páll]

Hi Ana Marija,

This seems to have little or nothing to do with PLUMED. Given the
presentation it is quite unclear to me:
i) what exactly is the issue (grompp segfault?); what happens if you use
unmodified GROMACS source? What if you run on the login node (binaries
compiled for it). Do other tools, e.g. mdrun work?
ii) Where are these build steps from, they look strange (e.g. you shouldn't
have to set MPI_LIBRARY or symlink libsci_gnu).

BTW, you can generate your tpr input locally or anywhere else, you don't
need to do it on the machine where you're planning ot run int.

Cheers,
--
Szilárd

On Wed, Oct 21, 2015 at 5:20 PM, Ana Marija 
wrote:

> Hi,
>
> I installed gromacs 4.6.7 with plumed like this:
> module swap PrgEnv-cray PrgEnv-gnu
> module load fftw/3.3.4.0
> module load cray-mpich/7.0.5
> module load gsl/1.15
> module load cmake
> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>
> mkdir lib2
>
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>
> tar zxvf plumed-2.2.0.tgz
> cd plumed-2.2.0
>
> ./configure CC=cc CXX=CC F77=ftn
> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> --disable-basic-warnings --disable-openmp
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> CC=cc
> FC=gfortran
> LDF90=gfortran
> CFLAGS=-g -O2
> CXX=CC
> CXXFLAGS=-O -fPIC
> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> LDFLAGS=
> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> ###
>
> make
> make install
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/new/modulefiles/)
> #2. Copy file: cp
> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> #4. type "module load plumed/2.2.0"
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> module use /lustre/beagle2/ams/new/modulefiles/
> module load plumed/2.2.0
>
> ### instal gromacs 4.6.7
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> tar zxvf gromacs-4.6.7.tar.gz
> cd gromacs-4.6.7/
> ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2
>
> Choose the best matching code/version:3
>
> mkdir build
> cd build
>
>
> export BUILD_WITH_INSTALL_RPATH=TRUE
> export INSTALL_RPATH=""
> export SKIP_BUILD_RPATH=TRUE
> export
>
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
>
> #in /lustre/beagle2/ams/new/gromacs make directory lib
>
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>
>
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF 

Re: [gmx-users] Temperature output file

[Justin Lemkul]

On 10/22/15 9:01 AM, Ali Mohyeddin wrote:

Dear all,

I am very beginner to gromacs. I have already simulated a simple protein
using a nice gromacs tutorial.
(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
)
Now I want to run some analysis to get the temperatures of protein and
solvent separately. I have entered the following command but nothing
written in temperature.xvg file:

gmx traj  -f  md_0_1.xtc  -s  md_0_1.tpr  -ot  temperature.xvg

May anyone help me?



There are no velocities in an .xtc file, so temperature can't be calculated. 
Moreover, you have to correct for the influence of constraints.


Simply put, you're using the wrong program for something simple like this.  What 
you want is gmx energy, as all temperature data are stored in the .edr file.


-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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Virtual Sites + Capped Termini

[Joan Clark Nicolas]

Dear gmx users,

I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
termini and using Virtual Sites.
When I try to generate the tpr file with grompp, it seems that it is
missing some constraint parameters for the bonds of C from ACE and N from
NME with their respective virtual sites. The error I am receiving is the
one that follows:


*ERROR 1 [file topol.top, line 8967]:*
*  No default Constr. No Conn. types*


*ERROR 2 [file topol.top, line 8968]:*
*  No default Constr. No Conn. types*


*ERROR 3 [file topol.top, line 9505]:*
*  No default Constr. No Conn. types*


*ERROR 4 [file topol.top, line 9506]:*
*  No default Constr. No Conn. types*

where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
correspond to NME N-VS bonds. Can you tell me what am I doing wrong?

Thank you very much!

*Joan Clark i Nicolas*
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

also I tried to install it with difference versions of gcc:
gcc/4.7.2  gcc/4.8.1  gcc/4.9.1  gcc/4.9.2

but segmentation error is still the same

On Wed, Oct 21, 2015 at 10:20 AM, Ana Marija 
wrote:

> Hi,
>
> I installed gromacs 4.6.7 with plumed like this:
> module swap PrgEnv-cray PrgEnv-gnu
> module load fftw/3.3.4.0
> module load cray-mpich/7.0.5
> module load gsl/1.15
> module load cmake
> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>
> mkdir lib2
>
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>
> tar zxvf plumed-2.2.0.tgz
> cd plumed-2.2.0
>
> ./configure CC=cc CXX=CC F77=ftn
> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> --disable-basic-warnings --disable-openmp
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> CC=cc
> FC=gfortran
> LDF90=gfortran
> CFLAGS=-g -O2
> CXX=CC
> CXXFLAGS=-O -fPIC
> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> LDFLAGS=
> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> ###
>
> make
> make install
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/new/modulefiles/)
> #2. Copy file: cp
> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> #4. type "module load plumed/2.2.0"
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> module use /lustre/beagle2/ams/new/modulefiles/
> module load plumed/2.2.0
>
> ### instal gromacs 4.6.7
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> tar zxvf gromacs-4.6.7.tar.gz
> cd gromacs-4.6.7/
> ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2
>
> Choose the best matching code/version:3
>
> mkdir build
> cd build
>
>
> export BUILD_WITH_INSTALL_RPATH=TRUE
> export INSTALL_RPATH=""
> export SKIP_BUILD_RPATH=TRUE
> export
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
>
> #in /lustre/beagle2/ams/new/gromacs make directory lib
>
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>
>
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON
>
>
> make
> make install
>
> I am getting Segmentation error if I run it like this:
>
> #!/bin/bash
> #PBS -N test
> #PBS -j oe
> #PBS -l 

[gmx-users] Temperature output file

[Ali Mohyeddin]

Dear all,

I am very beginner to gromacs. I have already simulated a simple protein
using a nice gromacs tutorial.
(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
)
Now I want to run some analysis to get the temperatures of protein and
solvent separately. I have entered the following command but nothing
written in temperature.xvg file:

gmx traj  -f  md_0_1.xtc  -s  md_0_1.tpr  -ot  temperature.xvg

May anyone help me?

Best regards,
Ali Mohyeddin
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[gmx-users] Turning off nonbonded interactions in protein-DNA

[Kartheek]

Dear all,
I am trying to do a simulation of protein-DNA complex by turning off all 
nonbonded interactions between protein and DNA, as suggested in the mailing 
list an "exclusions" section has been included in topology file. How do I know 
when I generate input file for mdrun whether these nonbonded interactions are 
turned off or not.

-- 
Sincerely,
P.Kartheek,
Research Scholar,
CCNSB,IIIT-Hyderabad.
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

Thanks. yes I will try to install this without using cross compiles, and I
am doing this on Cray XE6.

Will let you know the results.

Thanks you!

On Thu, Oct 22, 2015 at 10:19 AM, Szilárd Páll 
wrote:

> Please keep the discussion the list!
>
> There's a lot of information to parse here, I'll do my best, but I'm no
> interpreter so I may miss/misread something. :)
>
> Answers in-line.
>
> Note that in the GROMACS tool set only mdrun supports MPI, so, while
> typically it does not hurt, in general there is no benefit to building
> everything with MPI (and there is an mdrun-only target that can be used to
> build only mdrun with MPI).
>
> On Thu, Oct 22, 2015 at 4:46 PM, Ana Marija 
> wrote:
>
>> 1) if I run it via:
>> #!/bin/bash
>> #PBS -N test
>> #PBS -j oe
>> #PBS -l walltime=01:00:00
>> #PBS -l mppwidth=96
>>
>> source /opt/modules/default/init/bash
>>
>> cd $PBS_O_WORKDIR
>> module swap PrgEnv-cray PrgEnv-gnu
>> #export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>> #module use /lustre/beagle2/ams/new/modulefiles/
>> #module load plumed/2.2.0
>> export
>> LD_LIBRARY_PATH=/lustre/beagle2/gro/gromacs-4.6.7/build/lib:$LD_LIBRARY_PATH
>> export LD_LIBRARY_PATH=/opt/fftw/3.3.4.0/abudhabi/lib/:$LD_LIBRARY_PATH
>>
>> aprun -n 1 -N 1
>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi -f
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>
>> .tpr file is never generated instead I am gettig: core file
>> and in output file I have this error:
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>> _pmiu_daemon(SIGCHLD): [NID 00389] [c7-0c0s2n1] [Wed Oct 21 13:05:44
>> 2015] PE RANK 0 exit signal Segmentation fault
>>
>
> I doubt it's possible to tell why grompp segfaults and how to fix it (not
> without a backtrace or repro and further analysis). On our Cray (an XC30
> though) 4.6.7 grompp works fine on the compute nodes (also built with MPI).
>
>
> Other tools do work, I just can't get this input files.
>> those sym links are something I have to specify so that those libraries
>> can be found on our machine
>>
>
> Note that unless a user does something really exotic, there is little need
> for optimized BLAS/LAPACK libs (and there's intermal fallback code), but of
> course most of the time linking against libblas/liblapack won't hurt.
>
>
>> I am not sure I understand this:
>> "just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
>> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
>> login node."
>>
>> I did: export CC=gcc CXX=g++
>> before running grompp on login nodes via;
>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi -f
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>> and got Illegal instruction again
>>
>> so the problem is that I have in my
>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/ only grompp_mpi and that
>> can't run on login nodes
>>
>> did you mean I should do something different?
>>
>
> Yes, I did. You should use the regular C/C++ compiler to build programs
> that will run on the login node. So i was suggesting to reconfigure and
> compile using
> CC=gcc CXX=g++ cmake -DGMX_MPI=OFF [...] && make
> Depending on how the login nodes are configured you may also need to tweak
> the the instructions enabled, in particular, you _may_ have to
> set GMX_USE_RDTSCP=OFF at configure time.
>
> Let me know how that worked.
>
> Cheers,
> --
> Szilárd
>
>
>
>> On Thu, Oct 22, 2015 at 9:31 AM, Szilárd Páll 
>> wrote:
>>
>>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija >> > wrote:
>>>
 if I do that that I got: Illegal Instruction error
 which makes sense because I compiled gromacs with cross compiler for
 compute nodes

>>>
>>> just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
>>> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
>>> login node.
>>>
>>>

 On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W 
 wrote:

 > On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
 > > Hi,
 > >
 > > I installed gromacs 4.6.7 with plumed like this:
 > > module swap PrgEnv-cray PrgEnv-gnu
 > > module load fftw/3.3.4.0
 > > module load cray-mpich/7.0.5
 > > module load gsl/1.15
 > > module load cmake
 > > #in /lustre/beagle2/ams/new/gromacs make directory lib2
 > >
 > > mkdir lib2
 > >
 > > ams@login1:/lustre/beagle2/ams/lib2>ln -s
 > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
 > > 

[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Ebert Maximilian]

Dear list, 

I already asked the question in the AMBER list but couldn’t get an answer. So I 
try my luck here even though it is a bit off topic in the GROMACS list. I was 
wondering why the different atom types of H, C and O have different 
LJ-parameter but for all the different types of N we see the identical 
parameters in OPLS, AMBER and CHARMM?

Thank you very much,

Max
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Szilárd Páll]

Please keep the discussion the list!

There's a lot of information to parse here, I'll do my best, but I'm no
interpreter so I may miss/misread something. :)

Answers in-line.

Note that in the GROMACS tool set only mdrun supports MPI, so, while
typically it does not hurt, in general there is no benefit to building
everything with MPI (and there is an mdrun-only target that can be used to
build only mdrun with MPI).

On Thu, Oct 22, 2015 at 4:46 PM, Ana Marija 
wrote:

> 1) if I run it via:
> #!/bin/bash
> #PBS -N test
> #PBS -j oe
> #PBS -l walltime=01:00:00
> #PBS -l mppwidth=96
>
> source /opt/modules/default/init/bash
>
> cd $PBS_O_WORKDIR
> module swap PrgEnv-cray PrgEnv-gnu
> #export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> #module use /lustre/beagle2/ams/new/modulefiles/
> #module load plumed/2.2.0
> export
> LD_LIBRARY_PATH=/lustre/beagle2/gro/gromacs-4.6.7/build/lib:$LD_LIBRARY_PATH
> export LD_LIBRARY_PATH=/opt/fftw/3.3.4.0/abudhabi/lib/:$LD_LIBRARY_PATH
>
> aprun -n 1 -N 1 /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi
> -f /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>
> .tpr file is never generated instead I am gettig: core file
> and in output file I have this error:
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> _pmiu_daemon(SIGCHLD): [NID 00389] [c7-0c0s2n1] [Wed Oct 21 13:05:44 2015]
> PE RANK 0 exit signal Segmentation fault
>

I doubt it's possible to tell why grompp segfaults and how to fix it (not
without a backtrace or repro and further analysis). On our Cray (an XC30
though) 4.6.7 grompp works fine on the compute nodes (also built with MPI).


Other tools do work, I just can't get this input files.
> those sym links are something I have to specify so that those libraries
> can be found on our machine
>

Note that unless a user does something really exotic, there is little need
for optimized BLAS/LAPACK libs (and there's intermal fallback code), but of
course most of the time linking against libblas/liblapack won't hurt.


> I am not sure I understand this:
> "just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
> login node."
>
> I did: export CC=gcc CXX=g++
> before running grompp on login nodes via;
> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi -f
> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
> and got Illegal instruction again
>
> so the problem is that I have in my
> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/ only grompp_mpi and that
> can't run on login nodes
>
> did you mean I should do something different?
>

Yes, I did. You should use the regular C/C++ compiler to build programs
that will run on the login node. So i was suggesting to reconfigure and
compile using
CC=gcc CXX=g++ cmake -DGMX_MPI=OFF [...] && make
Depending on how the login nodes are configured you may also need to tweak
the the instructions enabled, in particular, you _may_ have to
set GMX_USE_RDTSCP=OFF at configure time.

Let me know how that worked.

Cheers,
--
Szilárd



> On Thu, Oct 22, 2015 at 9:31 AM, Szilárd Páll 
> wrote:
>
>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija 
>> wrote:
>>
>>> if I do that that I got: Illegal Instruction error
>>> which makes sense because I compiled gromacs with cross compiler for
>>> compute nodes
>>>
>>
>> just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
>> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
>> login node.
>>
>>
>>>
>>> On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W 
>>> wrote:
>>>
>>> > On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
>>> > > Hi,
>>> > >
>>> > > I installed gromacs 4.6.7 with plumed like this:
>>> > > module swap PrgEnv-cray PrgEnv-gnu
>>> > > module load fftw/3.3.4.0
>>> > > module load cray-mpich/7.0.5
>>> > > module load gsl/1.15
>>> > > module load cmake
>>> > > #in /lustre/beagle2/ams/new/gromacs make directory lib2
>>> > >
>>> > > mkdir lib2
>>> > >
>>> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s
>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s
>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>> > >
>>> > > tar zxvf plumed-2.2.0.tgz
>>> > > cd plumed-2.2.0
>>> > >
>>> > > ./configure CC=cc CXX=CC F77=ftn
>>> > > LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
>>> > > --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
>>> > > --disable-basic-warnings 

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

I installed it via:
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON

then I was running it on login nodes via:

/lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
/lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
/lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
/lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
/lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr


but I didn't get .tpr file, and output was this:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 1081 of the 1081 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 994 of the 1081 1-4 parameter combinations

---
Program grompp, VERSION 4.6.7
Source code file:
/lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803

Fatal error:
[ file tip3p.itp, line 39 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

can you please advise what should I do in this situation?

On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija 
wrote:

> so is it ok to try this?
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Your blas and lapack were compiled with gfortran, but in a way that they
>> require that one links further dependencies to use them later on. So
>> compile them better, or use dynamic linking.
>>
>> But 99.9% of GROMACS users do not need to get involved with this, so just
>> leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
>> internal versions.
>>
>> Mark
>>
>>
>
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Szilárd Páll]

On Thu, Oct 22, 2015 at 6:06 PM, Ana Marija 
wrote:

> so is it ok to try this?
>

Trying rarely hurts. :)


> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>


The CMKAE_SKIP_RPATH=ON part is only needed if you need/want to build
static binaries for the compute nodes.  As the Cray wrappers do some magic
behind the scenes in order to link statically, this ends up confusig cmake
which assumes that the resulting binaries will be dynamically linked.
Hence, the last step of setting the RPATH would fail (except if you tell
the Cray wrappers to stop the trickery and link dynamically: export
CRAYPE_LINK_TYPE=dynamic').

To build dynamically linked binaries for login nodes omitting RPATH is not
be necessary - and in fact it makes your/the users' life harder because
LD_LIBRARY_PATH will need to be set whenever running tools.



>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Your blas and lapack were compiled with gfortran, but in a way that they
> > require that one links further dependencies to use them later on. So
> > compile them better, or use dynamic linking.
> >
> > But 99.9% of GROMACS users do not need to get involved with this, so just
> > leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
> > internal versions.
> >
> > Mark
> >
> >
> --
> 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] gromacs 4.6.7 plumed -Segmentation fault

[Justin Lemkul]

On 10/22/15 12:34 PM, Ana Marija wrote:

I installed it via:
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON

then I was running it on login nodes via:

/lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
/lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
/lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
/lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
/lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr


but I didn't get .tpr file, and output was this:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 1081 of the 1081 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 994 of the 1081 1-4 parameter combinations

---
Program grompp, VERSION 4.6.7
Source code file:
/lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803

Fatal error:
[ file tip3p.itp, line 39 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

can you please advise what should I do in this situation?



The error message itself tells you the most likely problem.  Your topology has 
some formatting or sequence that is broken, causing misinterpretation or 
misapplication of a [ settles ] directive.


-Justin


On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija 
wrote:


so is it ok to try this?
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON



On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham 
wrote:


Hi,

Your blas and lapack were compiled with gfortran, but in a way that they
require that one links further dependencies to use them later on. So
compile them better, or use dynamic linking.

But 99.9% of GROMACS users do not need to get involved with this, so just
leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
internal versions.

Mark






--
==

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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Re: [gmx-users] suspension of colloids in GROMACS

[Justin Lemkul]

On 10/22/15 10:17 AM, CARDELLINI ANNALISA wrote:

Dear gromacs users,
In one project, I have to do some coarse grained molecular dynamics (CGMD)
simulations of nano-colloids (inorganic particles 100-150 nm, 3%wt max very
dilute) by using soft potentials (e.g. DLVO) and implicit solvent (Brownian
dynamics or fluctuating hydrodynamics).

1) I am wondering if GROMACS is the right tool for that... I mean, in principle,
it should be possible but is there explicit support for colloidal simulations?
How can we introduced a proper force field for particles interactions?



You may want to look into the MARTINI models for biomolecular systems.  The 
approach would be the same.  There is no need for "explicit support" for what 
you're doing; GROMACS is an MD engine, like any other.  If supplied a valid 
physical model, you can simulate anything.  GROMACS even handles planets :)


-Justin


2) Do you know someone in the GROMACS team doing colloidal simulations? Anyone
else in the World?

Your help would be highly appreciated.

Best regards,
Annalisa




Annalisa Cardellini, M.Sc.
Ph.D. student

E-mail: annalisa.cardell...@polito.it
SMaLL: http://www.polito.it/small


--
==

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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Re: [gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Justin Lemkul]

On 10/22/15 11:04 AM, Ebert Maximilian wrote:

Dear list,

I already asked the question in the AMBER list but couldn’t get an answer. So I 
try my luck here even though it is a bit off topic in the GROMACS list. I was 
wondering why the different atom types of H, C and O have different 
LJ-parameter but for all the different types of N we see the identical 
parameters in OPLS, AMBER and CHARMM?



Sometimes that's just the way force fields work out.  Electrostatics are tuned 
first, and then condensed phase interactions are targeted for LJ refinement. 
Given the nature of most N interactions (either lone pair or via polar/hydrogen 
bonding interactions with an H), the electrostatics generally dominate, so a 
generic LJ parameter that is common to different moieties is sufficient.


In CGenFF, there are several N types with different LJ, though the biomolecular 
parts of the CHARMM force field share the same parameters.


-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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Re: [gmx-users] Virtual Sites + Capped Termini

[Justin Lemkul]

On 10/22/15 9:05 AM, Joan Clark Nicolas wrote:

Dear gmx users,

I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
termini and using Virtual Sites.
When I try to generate the tpr file with grompp, it seems that it is
missing some constraint parameters for the bonds of C from ACE and N from
NME with their respective virtual sites. The error I am receiving is the
one that follows:


*ERROR 1 [file topol.top, line 8967]:*
*  No default Constr. No Conn. types*


*ERROR 2 [file topol.top, line 8968]:*
*  No default Constr. No Conn. types*


*ERROR 3 [file topol.top, line 9505]:*
*  No default Constr. No Conn. types*


*ERROR 4 [file topol.top, line 9506]:*
*  No default Constr. No Conn. types*

where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
correspond to NME N-VS bonds. Can you tell me what am I doing wrong?



Probably nothing, but not all constraint types are necessarily defined, 
especially for capped termini.  You will have to calculate appropriate 
[constrainttypes] for ffbonded.itp and add them.


-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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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Mark Abraham]

Hi,

Your blas and lapack were compiled with gfortran, but in a way that they
require that one links further dependencies to use them later on. So
compile them better, or use dynamic linking.

But 99.9% of GROMACS users do not need to get involved with this, so just
leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
internal versions.

Mark
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

so is it ok to try this?
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON



On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham 
wrote:

> Hi,
>
> Your blas and lapack were compiled with gfortran, but in a way that they
> require that one links further dependencies to use them later on. So
> compile them better, or use dynamic linking.
>
> But 99.9% of GROMACS users do not need to get involved with this, so just
> leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
> internal versions.
>
> Mark
>
>
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

after make step I am getting this errors gfortran related:

cunmqr.f:(.text+0x755): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrq.o): In function
`__sci_zunmrq_':
zunmrq.f:(.text+0x63e): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrq.o):zunmrq.f:(.text+0x6f6):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_po_complex_serial.o): In function
`irt_po_complex_serial_':
irt_po_complex_serial.f90:(.text+0x1294): undefined reference to
`_gfortran_os_error'
irt_po_complex_serial.f90:(.text+0x12a2): undefined reference to
`_gfortran_runtime_error'
/lustre/beagle2/ams/gro/lib/libblas.a(dormtr.o): In function
`__sci_dormtr_':
dormtr.f:(.text+0x322): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x4ea): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x549): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x589): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormqr.o): In function
`__sci_sormqr_':
sormqr.f:(.text+0x2e5): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormqr.o):sormqr.f:(.text+0x755):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_lu_complex_serial.o): In function
`irt_lu_complex_serial_':
irt_lu_complex_serial.f90:(.text+0x1299): undefined reference to
`_gfortran_os_error'
irt_lu_complex_serial.f90:(.text+0x12a7): undefined reference to
`_gfortran_runtime_error'
/lustre/beagle2/ams/gro/lib/libblas.a(shseqr.o): In function
`__sci_shseqr_':
shseqr.f:(.text+0x41a): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cgesvd.o): In function
`__sci_cgesvd_':
cgesvd.f:(.text+0x3fc): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0x5fb): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0x730): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(dormqr.o): In function
`__sci_dormqr_':
dormqr.f:(.text+0x2e5): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(dormqr.o):dormqr.f:(.text+0x73d):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(zunmql.o): In function
`__sci_zunmql_':
zunmql.f:(.text+0x43): undefined reference to
`_gfortran_get_environment_variable_i4'
zunmql.f:(.text+0x5c): undefined reference to `_gfortran_compare_string'
zunmql.f:(.text+0xbd): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormbr.o): In function
`__sci_sormbr_':
sormbr.f:(.text+0x3bf): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x58a): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x5e9): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x629): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqr.o): In function
`__sci_zunmqr_':
zunmqr.f:(.text+0x43): undefined reference to
`_gfortran_get_environment_variable_i4'
zunmqr.f:(.text+0x5c): undefined reference to `_gfortran_compare_string'
zunmqr.f:(.text+0xbd): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zgesvd3m.o): In function `zgesvd3m_':
zgesvd3m.f:(.text+0x35b): undefined reference to `_gfortran_concat_string'
zgesvd3m.f:(.text+0x4ef): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(irt_po_real_serial.o): In function
`irt_po_real_serial_':
irt_po_real_serial.f90:(.text+0x10e8): undefined reference to
`_gfortran_os_error'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrz.o): In function
`__sci_zunmrz_':
zunmrz.f:(.text+0x373): undefined reference to `_gfortran_concat_string'
zunmrz.f:(.text+0x744): undefined reference to `_gfortran_concat_string'
zunmrz.f:(.text+0x7f6): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cunmbr.o): In function
`__sci_cunmbr_':
cunmbr.f:(.text+0x3ab): undefined reference to `_gfortran_concat_string'
cunmbr.f:(.text+0x57e): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cunmbr.o):cunmbr.f:(.text+0x5d9):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_lu_real_serial.o): In function
`irt_lu_real_serial_':
irt_lu_real_serial.f90:(.text+0x107f): undefined reference to
`_gfortran_os_error'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqlint.o): In function
`zunmqlint_':
zunmqlint.f:(.text+0x63c): undefined reference to `_gfortran_concat_string'
zunmqlint.f:(.text+0x755): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqr_cray_internal.o): In function
`zunmqr_cray_internal_':
zunmqr_cray_internal.f:(.text+0x717): undefined reference to

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

where with "complete run" means I would run it later on compute nodes.

On Thu, Oct 22, 2015 at 11:58 AM, Ana Marija 
wrote:

> I just tried to install it with:
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF
>
> but the error is the same as above.
>
> My goal with this installation (without cross compiler) was to use it to
> generate input files and than use another installation of gromacs compiled
> with cross compilers to complete the run. Where I would use the same
> version of gromacs  in both cases, 4.6.7. Can you please confirm me that
> this is acceptable approach?
>
> The reason why I can't use newer version of gromacs is that I only have
> cmake 2.8.4 on this machine and it is impossible to install newer version
> of cmake because it is tied to gnu version we got from Cray etc.
>
>
>
> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll 
> wrote:
>
>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija 
>> wrote:
>>
>>> I installed it via:
>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>
>>> then I was running it on login nodes via:
>>>
>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>>
>>>
>>> but I didn't get .tpr file, and output was this:
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>>> Generated 1081 of the 1081 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 994 of the 1081 1-4 parameter combinations
>>>
>>> ---
>>> Program grompp, VERSION 4.6.7
>>> Source code file:
>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>>
>>> Fatal error:
>>> [ file tip3p.itp, line 39 ]:
>>> Atom index (1) in settles out of bounds (1-0).
>>> This probably means that you have inserted topology section "settles"
>>> in a part belonging to a different molecule than you intended to.
>>> In that case move the "settles" section to the right molecule.
>>>
>>> can you please advise what should I do in this situation?
>>>
>>
>> As Justin said, this isn't an issue with the GROMACS build anymore (but
>> rather with the inputs). So it seems that the original problem is solved -
>> unless you really need to run grompp on the compute nodes.
>>
>> BTW, I hope you know that 4.6.7 is a rather old and outdated version; the
>> 5.0 and 5.1 series has been released since and the former is AFAIK
>> supported by PLUMED!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>>>
>>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
>>> sokovic.anamar...@gmail.com> wrote:
>>>
 so is it ok to try this?
 cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
 -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
 -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
 -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
 -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
 -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON



 On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
 mark.j.abra...@gmail.com> wrote:

> Hi,
>
> Your blas and lapack were compiled with gfortran, but in a way that
> they require that one links further dependencies to use them later on. So
> compile them better, or use dynamic linking.
>
> But 99.9% of GROMACS users do not need to get involved with this, so
> just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use 
> its
> internal versions.
>
> Mark
>
>

>>>
>>
>
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