[gmx-users] nstcomm < nstcalenergy

[Simon Kit Sang Chu]

Dear every user,

I am using Andersen thermostat and nstcomm should be set to 1 (step).
However, after specifying nstcomm = 1, an error has returned -

nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it
to nstcalenergy step.


I fail to search for "nstcalenergy" in neither mdp nor manual.

I am asking again since I did not receive any reply on my previous post.
Sorry for my annoyance.

Regards,
Simon
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[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Apramita Chand]

Dear All,
I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
4 -e 10 as options. The results came as









*ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) =
2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q
=  0--Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward-0.008
-126.851-666.000  2.8733*

(This came for both with and without pbc). I also tried to do it from the
g_hbond command itself by giving starting time as 40ns and ending as 100ns,
but again it came negative lifetime.


Next, I tried g_trjconv with application of -pbc mol -ur compact options on
untruncated(100ns) trajectory. The results came as:













*ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q
=  0--Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward 0.001
1793.775  23.259 3.03095*
When I tried the same with the original unconverted trajectory(without
g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*.






*My question is ,1) why do the truncated trajectories give negative values
for my simulation?*



*2)If I take the whole 100ns for analysis of hydrogen bond lifetime, which
value should I take, since application of pbc gives a different value than
that of the original trajectory value of lifetime.*
I would be very grateful for your help.
Looking forward to your suggestions


Yours sincerely
Apramita Chand
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Re: [gmx-users] gromacs error

[Neha Gupta]

Hi Vytautas,

Thank you for your response..

I did as you told and got this message at the command prompt

libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a

But the error tells me :

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

Even when I go to that location, namely, /usr/local/lib. I do not find "
libfftw3f.so.3."

What is the next step?

Thanks,
Neha

On Mon, Aug 28, 2017 at 12:33 PM, Vytautas Rakeviius  wrote:

>
> Make sure you have libfftw3f installed properly. In such case
> command:whereis libfftw3fshould give you location of that file which gmx is
> unable to find.
> On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta <
> nehaphysic...@gmail.com> wrote:
>
> Hi gromacs users,
>
> How to fix this error?
>
> gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> PATH=$PATH:"/usr/local/gromacs/bin/"
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"
>
>
>
> Thanks,
> Neha
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Re: [gmx-users] RDF

[Dallas Warren]

No idea what a surface distribution function is, and how it is
generated.  But I suspect that those two are not the same.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 23 August 2017 at 14:27, RAHUL SURESH  wrote:
> Thank you Sir,
>
> Is spatial distribution function is same as that of surface distribution
> function?
>
> On Wed, Aug 23, 2017 at 9:39 AM, Dallas Warren 
> wrote:
>
>> https://www.google.com.au/search?q=gromacs+sdf
>>
>> i.e. gmx spatial
>>
>> Unfortunately, it only currently will work for a single reference
>> molecule.  There use to be a g_sdf that would work for multiple copies
>> of the reference, much in the same manner that gmx rdf does.  So if
>> that is what you are after, you will need to install that older
>> version and use that to generate it.
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> -
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>> On 23 August 2017 at 13:27, RAHUL SURESH  wrote:
>> > Dear Warren,
>> >
>> > Thanks a lot. How will I be able to calculate SDF using Gromacs..?
>> >
>> >
>> >
>> > On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren 
>> > wrote:
>> >
>> >> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
>> >> So instead of simply having a probability associated with each radius
>> >> (r), it provides a probability associated with each (x,y,z) point.
>> >>
>> >> VMD can display the SDF generated by GROMACS.
>> >> Catch ya,
>> >>
>> >> Dr. Dallas Warren
>> >> Drug Delivery, Disposition and Dynamics
>> >> Monash Institute of Pharmaceutical Sciences, Monash University
>> >> 381 Royal Parade, Parkville VIC 3052
>> >> dallas.war...@monash.edu
>> >> -
>> >> When the only tool you own is a hammer, every problem begins to
>> resemble a
>> >> nail.
>> >>
>> >>
>> >> On 18 August 2017 at 21:47, RAHUL SURESH 
>> wrote:
>> >> > Hi Dan
>> >> >
>> >> > Thank you so much for you descriptive answers. I have few
>> clarifications
>> >> > that I have posted here. I will go through the papers here.
>> >> >
>> >> > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil 
>> wrote:
>> >> >
>> >> >> Hi Rahul,
>> >> >>
>> >> >> I can't find the exact papers right now, but I remember seeing some
>> >> >> inconsistency in how people name these functions especially the
>> radial
>> >> >> distribution function and pair correlation functions.
>> >> >>
>> >> >> If we go far back into literature, we can see JG Kirkwood using pair
>> >> >> correlation functions as functions of both the distance and the
>> relative
>> >> >> orientation between the pairs [The Journal of Chemical Physics 19,
>> 774
>> >> >> (1951); doi: 10.1063/1.1748352]. I don't know if he is the
>> "inventor" of
>> >> >> the RDF, but he was one of the earliest to use it extensively in
>> >> theories.
>> >> >> When you average the pair correlation functions over the relative
>> >> >> orientations, you get the radial distribution function which is a
>> >> function
>> >> >> of distance only.
>> >> >
>> >> >
>> >> > That was very informative. But as now it can be calculated as a whole
>> >> > easily using various tools.
>> >> >
>> >> >
>> >> >> I think I've seen newer papers use RDF/PCF/PDF somewhat
>> >> >> interchangeably although I can't find these right now... Most people
>> >> mean
>> >> >> the RDF but you can always look at the data to know what they mean.
>> >> >>
>> >> >
>> >> > I have come across people describing RDF analysis between water and
>> water
>> >> > and I always wonder what does it means. RDF can be done between
>> protein
>> >> and
>> >> > water to know the distribution of water around protein with default
>> >> center
>> >> > of mass(My little knowledge) and what co-ordination number contribute
>> to
>> >> > RDF has always been a puzzle for me.
>> >> >
>> >> >>
>> >> >> I never used surface distribution functions, hopefully someone else
>> can
>> >> >> bring you up to date on that one (How is the surface defined?).
>> >> >>
>> >> >
>> >> > I will be happy if some one can explain SDF and any particular tool to
>> >> > analyze it.
>> >> >
>> >> >>
>> >> >> But there is also the spatial distribution functions, which now a
>> >> function
>> >> >> in 3D spherical coordinates. It gives the average density of
>> particles
>> >> at
>> >> >> given (r, theta, phi). In this paper they normalize it by the bulk
>> >> density,
>> >> 

[gmx-users] Surface Tension Calculation

[Lei]

Hi, gmx users,
I have some questions regarding the surface tension calculation in gromacs.
I was running simulations about interface between phase 1 (solid) and phase
2 (liquid). In my production run, the phase 1 molecules are frozen and I
need to calculate the interfacial tension between phase 1 and phase 2.  I
followed the typical procedure to calculate the surface tension: phase 1 is
sandwiched by phase 2 and the interface is planar.
So my questions are:
1. Is there a way to calculate the interfacial tension between phase 1 and
phase 2?
2. Does the freeze command affect the calculation of tension? Do I need to
freeze phase 1 atoms in the simulation to calculate the interfacial tension
between phase 1 and phase 2?
3. What if I applied the position restraints on the phase 1 atoms instead
of freezing them?
Thank you all and enjoy simulating.
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Re: [gmx-users] Corrupted checkpoint file from MD simulation

[melichercik]

Hi,
if you have .trr with saved velocities (at least from time to time), you can 
create new tpr file starting with the last frame you have.
Command: gmx tpbconv -s .tpr -f .trr -e .edr -time 
 -o .tpr

And with this new .tpr you'll start normal run (gmx mdrun ...) and than you 
have to concatenate files with gmx eneconv and gmx trjcat. At least the version 
4.x required at least the velocities and energies for some frame and I don't 
think it is possible to continue without them (cause of nature of MD).
Good luck.

Milan

On Mon, Aug 28, 2017 at 10:50:09AM -0500, Alexander Yang wrote:
> Hi everyone,
> 
> Recently, I was running a simulation on a computer cluster, but the
> computer cluster unexpectedly crashed. The trajectory file (.xtc) was
> saved, but the checkpoint files (both .cpt and _prev.cpt) seem to be
> corrupted. Does anyone have any recommendations on continuing the
> trajectory despite the corrupted checkpoint files?
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[gmx-users] Corrupted checkpoint file from MD simulation

[Alexander Yang]

Hi everyone,

Recently, I was running a simulation on a computer cluster, but the
computer cluster unexpectedly crashed. The trajectory file (.xtc) was
saved, but the checkpoint files (both .cpt and _prev.cpt) seem to be
corrupted. Does anyone have any recommendations on continuing the
trajectory despite the corrupted checkpoint files?
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Re: [gmx-users] problem installing plumed-2.3.2

[Giovanni Bussi]

Hi,

please post these questions to plumed mailing list.

You should check the name of your MPI compiler and pass it to configure as
CXX=name/of/the/compiler

Giovanni

On Mon, Aug 28, 2017 at 3:36 PM,  wrote:

> Hii all
>I am trying to install plumed-2.3.2 in CRAY system. I am using this
> command to configure plumed
>  ./configure --enable-mpi --prefix=/work/plumed-2.2.5/
> At the end it shows a warning
>
>  configure: WARNING:  PLUMED will NOT be compiled using MPI because MPI
> have not been found!
> configure: creating ./config.statusconfig.status: creating
> Makefile.conf
>   config.status: creating sourceme.sh
>   config.status: creating stamp-h
>
> How to solve this problem? I want to use it with MPI support.
> Thank you..
>
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-- 
Giovanni Bussi
Scuola Internazionale Superiore di Studi Avanzati - SISSA
via Bonomea 265, 34136 Trieste, Italy
email: bu...@sissa.it
web:   http://people.sissa.it/~bussi
  http://srnas.sissa.it
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[gmx-users] problem installing plumed-2.3.2

[spss4]

Hii all
   I am trying to install plumed-2.3.2 in CRAY system. I am using this
command to configure plumed
 ./configure --enable-mpi --prefix=/work/plumed-2.2.5/
At the end it shows a warning 

 configure: WARNING:  PLUMED will NOT be compiled using MPI because MPI
have not been found!
configure: creating ./config.statusconfig.status: creating
Makefile.conf
  config.status: creating sourceme.sh
  config.status: creating stamp-h
   
How to solve this problem? I want to use it with MPI support. 
Thank you..
  
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Re: [gmx-users] Trouble with gmx distance

[Sotirios Dionysios I. Papadatos]

Wow! It worked!!! Thank you so much. It just needed to pass both choices in one 
line. Thanks again.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Vytautas 
Rakeviius 
Sent: Monday, August 28, 2017 11:28:54 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Trouble with gmx distance

Two atoms for distance calculation have to be in same selection thus program 
expects even number of positions and do not get in my opinion.You could show 
your index.ndx for better investigation.



On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos 
 wrote:

Hi, I am trying to calculate the distance between two atoms, which are defined 
in an index file. The command that I use is:

"gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg"

I get the obvious:

"Selection 'atom_name' does not evaluate into an even number of positions (there

are 1 positions)"
The same happens if I use in -f prod.trr
What might be wrong? Any insights on what to look for? What usually gives this 
kind of error?
Feel free to ask for any further information.
Thanks in advance
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Re: [gmx-users] Error with MPICH

[Szilárd Páll]

That kind of cmake invocation with MPI on without setting the
compilers to the MPI wrappers can often fail depending on how well the
MPI installation is detected by cmake. Try setting CMAKE_C_COMPILER
and CMAKE_CXX_COMPILER variables to the MPI compiler wrappers, i.e.
mpicc/mpic++ or similar.
--
Szilárd


On Fri, Aug 18, 2017 at 2:34 PM, Souparno Adhikary
 wrote:
> My CMAKE was like this:
>
> /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
>
> I have compiled mpich2 with --enable-shared option.
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Fri, Aug 18, 2017 at 6:01 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> If libmpich.so is available after building with --enabled-shared, then the
>> MPI wrapper compilers should take care of this. If you want more help, we
>> need to at least see how you called cmake, using mpicc and mpic++, and more
>> information about what was wrong than "it still doesn't work." :-)
>>
>> Mark
>>
>> On Fri, Aug 18, 2017 at 12:02 PM Souparno Adhikary 
>> wrote:
>>
>> > Hi,
>> >
>> > I was installing GROMACS-5.1.4 with MPI option in the server. It yielded
>> > the following error,
>> >
>> > [  6%] Linking CXX shared library ../../lib/libgromacs_mpi.so
>> > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
>> R_X86_64_32
>> > against `.rodata.str1.8' can not be used when making a shared object;
>> > recompile with -fPIC
>> > /usr/local/lib/libmpich.a: could not read symbols: Bad value
>> > collect2: ld returned 1 exit status
>> > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
>> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> > make: *** [all] Error 2
>> >
>> > As the available suggestions on the internet suggested, I recompiled the
>> > mpich with --enable-shared option and also setting the CXXFLAGS as -fPIC.
>> > It still doesn't work.
>> >
>> > Can you please help?
>> >
>> > Souparno Adhikary,
>> > CHPC Lab,
>> > Department of Microbiology,
>> > University of Calcutta.
>> > --
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>> >
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Re: [gmx-users] Performance values

[Szilárd Páll]

On Mon, Aug 7, 2017 at 6:10 PM, Maureen Chew  wrote:
> Szilárd,
> Thank you so very much for the reply!You mention
> that time/step is important if trying to do an apples-to-apples
> comparison for any given simulation.
>
> I have a few questions - For specific example, use the RNAse reference here:
> (http://www.gromacs.org/gpu )
> Influence of box geometry and virtual interaction sites
> This is a simulation of the protein RNAse, which contains roughly 24,000 
> atoms in a cubic box.
> The image rnase.png , 
> shows a 6 core baseline to be, roughly 50ns/day
>
> First,  assuming this is from rnase_cubic @ 
> ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz 
> 
> which contains these files:
> rnase_cubic/rf_verlet.mdp
> rnase_cubic/conf.gro
> rnase_cubic/topol.top
> rnase_cubic/pme_verlet.mdp
> 3 questions:
> - What gmx grompp command was use to generate the tpr file for the result in 
> rnase.png?

Those are two sets of runs, the first four use the cubic RNAse setup
without virtual sites (i.e. the inputs you list above) and the "PME"
mdp settings file, so you need to do
gmx grompp -f pme_verlet

The latter four bars use the other input for which you'll need a
command line similar to the above to set up, but using the appropriate
input files from the "rnase_dodec_vsites" tarball.

> Apologies if its intuitively obvious which mdp  was used
> - Aside from -ntmpi and -ntomp parms, what gmx mdrun command was used to 
> obtain
> the 6 core result?

In all single-node (and single-GPU) runs OpenMP-only parallelization
is used, i.e. 1 MPI rank and as many OpenMP threads as hardware
threads, i.e. for the 6-core run "mdrun -ntmpi 1 -ntomp 12" (which is
also the default).

Note that the date you're looking at is several years old by now and
was collected on an Intel Sandy Bridge-E CPU (i7-3930K), so it is not
highly representative of the current performance of GROMACS.

> - From that 6 core run, what is the time/step that you refer to?

Have a look in the "dt" field in the mdp or log file; in this case
dt=0.002, i.e 2 fs. For the vsites case it is 5 fs.

> Is that
> real cycle  and time accounting for neighbor search, force, PME mesh 
> etc,
> and  time/step that you refer to is the wall time/call count?

Note sure if I understand the question, but I'll try to answer it:
that is simulation time/wall time, i.e. number of time-steps * dt /
wall-t in days.


Cheers,
--
Szilárd


> Thanks in advance!
> —maureen
>
>
> Date: Mon, 7 Aug 2017 16:01:16 +0200
> From: Szilárd Páll >
> To: Discussion list for GROMACS users  >
> Subject: Re: [gmx-users] Performance values
>
>
> Indeed, "Wall t" is real application wall-time, nanoseconds/day is the
> typical molecular dynamics performance unit that corresponds to the
> effective amount of simulation throughput (note that this however
> depends on the time-step and without that specified it is not useful
> to compare to other runs), so often it is useful to use it convert it
> to time/step.
> --
> Szilárd
>
>
> On Fri, Jul 28, 2017 at 10:20 AM, Maureen Chew  > wrote:
>> You might find this reference handy - it has a really nice explanation for 
>> how to look
>> at a log file
>> Topology preparation, "What's in a log file", basic performance 
>> improvements: Mark Abraham, Session 1A 
>> >  
>> >
>>
>> The ?Performance:? values are a throughput measure where both values 
>> represent
>> the same thing in different terms.  In your sample below, 3.964 is the
>> number of nanoseconds that can be simulated in 24 hours while it takes
>> 6.054 hours to simulate 1 ns
>>
>> HTH
>>
>>
>> On Jul 27, 2017, at 10:15 AM, Maureen Chew > > wrote:
>>> Where is it documented how the mdrun performance metrics are calculated ? 
>>> I?ve
>>> looked here
>>> http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
>>>  
>>> 
>>>  
>>> >>  
>>> >
>>> and here
>>> 

Re: [gmx-users] ERROR IN EXECUTION ---GMX

[Tasneem Kausar]

If you are using linux and gromacs is installed in /user/local/bin check
these steps

vi ~/.bashrc
in the last line of the file add
source /usr/local/bin/GMXRC

and save this.






On Mon, Aug 28, 2017 at 12:08 PM, Neha Gupta 
wrote:

> Hi,
>
> I gave these commands initially
>
> PATH=$PATH:"/usr/local/gromacs/bin/"  (this mentions path to gmx)
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"
>
> For that, I got the response,
>
> gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> I went through "lib" folder (had mentioned its contents above)  and lib64
> which contains libgromacs.so.0.0.0
>
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Trouble with gmx distance

[Vytautas Rakeviius]

Two atoms for distance calculation have to be in same selection thus program 
expects even number of positions and do not get in my opinion.You could show 
your index.ndx for better investigation.



On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos 
 wrote:

Hi, I am trying to calculate the distance between two atoms, which are defined 
in an index file. The command that I use is:

"gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg"

I get the obvious:

"Selection 'atom_name' does not evaluate into an even number of positions (there

are 1 positions)"
The same happens if I use in -f prod.trr
What might be wrong? Any insights on what to look for? What usually gives this 
kind of error?
Feel free to ask for any further information.
Thanks in advance
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Re: [gmx-users] QM/MM simulation (Mostafa Javaheri)

[Groenhof, Gerrit]

Hi,

Could it be that the QM level of theory is not suited (candidates are charge 
and multiplicity) for the QM subsystem? What happens if you run a QM only 
calculation on your QM system ?

Gerrit

 Dear gmx users
I'm doing an QM/MM simulation of a ligand-protein system by the Gromacs
ORCA interface. When I set constraint = none in the Gromacs mdp file the
bonds' length of the atoms oscillate extremely even those that did not
index as the QM atoms e.g. aromatic rings will be twisted during the mdrun
and when I set constraint = all-bonds I get this error ?Step 1, time 0.002
(ps) LINCS WARNING relative constraint deviation after LINCS? I thinks this
happens because I constrained the reactant atoms explicitly in the topology
file. Are these kind of oscillations usual in QM/MM simulations?
Note When I set QMMM = No in the mdp file no unusual vibration happens. Any
help will be appreciated.
Sincerely
M.Javaheri


Could it be that the level of QM theory is not 


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End of gromacs.org_gmx-users Digest, Vol 160, Issue 128
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Re: [gmx-users] gromacs error

[Vytautas Rakeviius]

Make sure you have libfftw3f installed properly. In such case command:whereis 
libfftw3fshould give you location of that file which gmx is unable to find.
On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta 
 wrote:

Hi gromacs users,

How to fix this error?

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

PATH=$PATH:"/usr/local/gromacs/bin/"

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"



Thanks,
Neha
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Re: [gmx-users] Unable to install 5.1.14

[Vytautas Rakeviius]

You have updated boost so you have to update GROMACS too. 2016.3 is the latest 
version you should download it.
Another possibility is to downgrade boost to older, but you can bump into other 
mish-mash issues. I do not recommend that.



On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat Desikan 
 wrote:

Dear All,
I had removed gromacs 5.1.14. from my system (Ubuntu 16.04) a while ago,
and I'm having trouble reinstalling it. Cmake runs fine, but the system
repeatedly fails in the make step with this weird error:

[  3%] Building CXX object src/gromacs/CMakeFiles/
libgromacs.dir/listed-forces/pairs.cpp.o
[  3%] Building CXX object src/gromacs/CMakeFiles/
libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o
In file included from /usr/local/include/boost/exception/detail/exception_
ptr.hpp:20:0,
                from /usr/local/include/boost/exception_ptr.hpp:9,
                from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
utility/exceptions.h:53,
                from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.cpp:62:
/usr/local/include/boost/exception/info.hpp: In member function ‘virtual
boost::shared_ptr
boost::exception_detail::error_info_container_impl::get(const
boost::exception_detail::type_info_&) const’:
/usr/local/include/boost/exception/info.hpp:102:28: error: use of deleted
function 
‘boost::shared_ptr::shared_ptr(const
boost::shared_ptr&)’
                    return p;
                            ^
In file included from /usr/local/include/boost/shared_ptr.hpp:17:0,
                from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.h:54,
                from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.cpp:47:
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:168:25: note:
‘boost::shared_ptr::shared_ptr(const
boost::shared_ptr&)’ is
implicitly declared as deleted because ‘boost::shared_ptr’ declares a move constructor or move
assignment operator

There are similar errors after this, and make fails. I have updated boost
on my system (version 58), and my system has the latest upgrades. Can
anyone please point out the way ahead? I've exhausted all easy options (Eg.
cleanly remove all gromacs associated files, redownload, untar and try to
install).

My cmake command is:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs514 -DGMX_USE_RDTSCP=off

I've tried other permutations of the above command (without
-DGMX_USE_RDTSCP=off
for instance) and nothing seems to work.

Thank you for your time.

Regards,
Rajat

-- 
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] ERROR IN EXECUTION ---GMX

[Neha Gupta]

Hi,

I gave these commands initially

PATH=$PATH:"/usr/local/gromacs/bin/"  (this mentions path to gmx)

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"

For that, I got the response,

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

I went through "lib" folder (had mentioned its contents above)  and lib64
which contains libgromacs.so.0.0.0


Thanks,
Neha
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