Re: [gmx-users] problems with the output of pullx

2018-02-24 Thread alfredo 

Hi Mark,

Thanks for your comment. No, that is not the problem. At that location 
the center of mass of the peptide is deep inside the membrane, 
separation between the two pulling groups is 0.4 nm and the dimension of 
the cell along z is more than 10 nm. I am only pulling along the z 
direction. The puzzle to me is that when I extract the center of mass 
separation along z between the same two groups using gmx traj those 
spikes don't show up at the times when they are shown in the pullx file.


Alfredo



On 2018-02-24 11:57, Mark Abraham wrote:

Hi,

My (thoroughly uneducated) guess is that the spikes are related to the 
pull
distance approaching half of the dimensions of the cell. Not all 
flavours

of pulling can  handle this. Might that be the issue?

Mark

On Sat, Feb 24, 2018, 17:55 alfredo  wrote:


Hi,
Updating my post. The problem has been observed in two different 
machine

systems (the latest I have found the problem was the skylake nodes in
tacc). I assumed it has to be some communication bug of coordinates 
and

forces in the pull part of the code. Probably observed in my case
because of the large size of the peptide I am pulling inside the
membrane. For now I am thinking to extract coordinates from the trr 
file

and from them compute the pulling harmonic forces. But not an ideal
solution.
Thanks
Alfredo




On 2018-02-22 10:17, Alfredo E. Cardenas wrote:
> Hi,
> I am using gromacs to get the PMF of a peptide of  about 20 amino
> acids, moving inside of a bilayer membrane. After pulling the peptide
> inside the membrane now I am using  pull-coord1-type = umbrella
> and pull-coord1-geometry  = distance to sample configurations in each
> window for the umbrella simulations along the z axis (axis
> perpendicular to the membrane surface). Runs finish ok, no error
> messages. The problem is that when I looked at the contents of the
> pullx file I observed spikes (up to 5 or more Angstroms) in the z
> coordinate separating the center of mass of the peptide from the
> membrane center. But when I extract the z coordinates of the center of
> mass of the two groups and compute the difference the values look
> reasonable with no spikes.
>
> Here an example (it starts good):
>   time (ps)   from pullx  from traj analysis
>
>20.000  0.475923002  0.475919992
>200010.000  0.498394012  0.498389989
>200020.000  0.527589977  0.527589977
>200030.000  0.491834015  0.493739992
>200040.000  0.485377997  0.485379994
>200050.000  0.488474995  0.488469988
>200060.000  0.507991016  0.507990003
>200070.000  0.475095987  0.475100011
>200080.000  0.465889990  0.465889990
>200090.000  0.515878975  0.515879989
>200100.000  0.501435995  0.501429975
>200110.000  0.505191982  0.505190015
>
> Here a bad section:
>
>214000.000  0.427343011  0.601450026
>214010.000  0.484564990  0.545799971
>214020.000  0.530139029  0.603110015
>214030.000  0.176231995  0.650319993
>214040.000  0.342045009  0.637109995
>214050.000  0.181202993  0.636659980
>214060.000  0.338808000  0.595300019
>214070.000  0.442301005  0.547529995
>214080.000  0.396046013  0.565050006
>214090.000  0.431407988  0.538460016
>214100.000  0.402586013  0.56825
>214110.000  0.438223004  0.575810015
>
> Then good again:
>
>23.000  0.477869004  0.477869987
>230010.000  0.511840999  0.511839986
>230020.000  0.469146013  0.469150007
>230030.000  0.480194002  0.480190009
>230040.000  0.525618017  0.525619984
>230050.000  0.498955995  0.498950005
>230060.000  0.489230990  0.489230007
>230070.000  0.531931996  0.531930029
>230080.000  0.535376012  0.535380006
>230090.000  0.488822013  0.48883
>230100.000  0.510704994  0.510699987
>230110.000  0.524537981  0.524540007
>230120.000  0.513199985  0.513189971
>
> This problem happens in most umbrella windows that I have examined,
> sometimes several times during the long trajectories I am running. The
> pullf output also have those spikes.
>
> Here is the mdp file I am using:
>
> integrator  = md
> dt  = 0.002
> nsteps  = 5000
> nstlog  = 1
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstcalcenergy   = 500
> nstenergy   = 500
> ;
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> coulombtype = pme
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw

Re: [gmx-users] problems with the output of pullx

2018-02-24 Thread Mark Abraham 
Hi,

My (thoroughly uneducated) guess is that the spikes are related to the pull
distance approaching half of the dimensions of the cell. Not all flavours
of pulling can  handle this. Might that be the issue?

Mark

On Sat, Feb 24, 2018, 17:55 alfredo  wrote:

> Hi,
> Updating my post. The problem has been observed in two different machine
> systems (the latest I have found the problem was the skylake nodes in
> tacc). I assumed it has to be some communication bug of coordinates and
> forces in the pull part of the code. Probably observed in my case
> because of the large size of the peptide I am pulling inside the
> membrane. For now I am thinking to extract coordinates from the trr file
> and from them compute the pulling harmonic forces. But not an ideal
> solution.
> Thanks
> Alfredo
>
>
>
>
> On 2018-02-22 10:17, Alfredo E. Cardenas wrote:
> > Hi,
> > I am using gromacs to get the PMF of a peptide of  about 20 amino
> > acids, moving inside of a bilayer membrane. After pulling the peptide
> > inside the membrane now I am using  pull-coord1-type = umbrella
> > and pull-coord1-geometry  = distance to sample configurations in each
> > window for the umbrella simulations along the z axis (axis
> > perpendicular to the membrane surface). Runs finish ok, no error
> > messages. The problem is that when I looked at the contents of the
> > pullx file I observed spikes (up to 5 or more Angstroms) in the z
> > coordinate separating the center of mass of the peptide from the
> > membrane center. But when I extract the z coordinates of the center of
> > mass of the two groups and compute the difference the values look
> > reasonable with no spikes.
> >
> > Here an example (it starts good):
> >   time (ps)   from pullx  from traj analysis
> >
> >20.000  0.475923002  0.475919992
> >200010.000  0.498394012  0.498389989
> >200020.000  0.527589977  0.527589977
> >200030.000  0.491834015  0.493739992
> >200040.000  0.485377997  0.485379994
> >200050.000  0.488474995  0.488469988
> >200060.000  0.507991016  0.507990003
> >200070.000  0.475095987  0.475100011
> >200080.000  0.465889990  0.465889990
> >200090.000  0.515878975  0.515879989
> >200100.000  0.501435995  0.501429975
> >200110.000  0.505191982  0.505190015
> >
> > Here a bad section:
> >
> >214000.000  0.427343011  0.601450026
> >214010.000  0.484564990  0.545799971
> >214020.000  0.530139029  0.603110015
> >214030.000  0.176231995  0.650319993
> >214040.000  0.342045009  0.637109995
> >214050.000  0.181202993  0.636659980
> >214060.000  0.338808000  0.595300019
> >214070.000  0.442301005  0.547529995
> >214080.000  0.396046013  0.565050006
> >214090.000  0.431407988  0.538460016
> >214100.000  0.402586013  0.56825
> >214110.000  0.438223004  0.575810015
> >
> > Then good again:
> >
> >23.000  0.477869004  0.477869987
> >230010.000  0.511840999  0.511839986
> >230020.000  0.469146013  0.469150007
> >230030.000  0.480194002  0.480190009
> >230040.000  0.525618017  0.525619984
> >230050.000  0.498955995  0.498950005
> >230060.000  0.489230990  0.489230007
> >230070.000  0.531931996  0.531930029
> >230080.000  0.535376012  0.535380006
> >230090.000  0.488822013  0.48883
> >230100.000  0.510704994  0.510699987
> >230110.000  0.524537981  0.524540007
> >230120.000  0.513199985  0.513189971
> >
> > This problem happens in most umbrella windows that I have examined,
> > sometimes several times during the long trajectories I am running. The
> > pullf output also have those spikes.
> >
> > Here is the mdp file I am using:
> >
> > integrator  = md
> > dt  = 0.002
> > nsteps  = 5000
> > nstlog  = 1
> > nstxout = 5000
> > nstvout = 5000
> > nstfout = 5000
> > nstcalcenergy   = 500
> > nstenergy   = 500
> > ;
> > cutoff-scheme   = Verlet
> > nstlist = 20
> > rlist   = 1.2
> > coulombtype = pme
> > rcoulomb= 1.2
> > vdwtype = Cut-off
> > vdw-modifier= Force-switch
> > rvdw_switch = 1.0
> > rvdw= 1.2
> > ;
> > tcoupl  = Nose-Hoover
> > tc_grps = PROT   MEMB   SOL_ION
> > tau_t   = 1.01.01.0
> > ref_t   = 303.15 303.15 303.15
> > ;
> > pcoupl  = Parrinello-Rahman
> > pcoupltype  = semiisotropic
> > tau_p   = 5.0
> > compre

Re: [gmx-users] problems with the output of pullx

2018-02-24 Thread alfredo 

Hi,
Updating my post. The problem has been observed in two different machine 
systems (the latest I have found the problem was the skylake nodes in 
tacc). I assumed it has to be some communication bug of coordinates and 
forces in the pull part of the code. Probably observed in my case 
because of the large size of the peptide I am pulling inside the 
membrane. For now I am thinking to extract coordinates from the trr file 
and from them compute the pulling harmonic forces. But not an ideal 
solution.

Thanks
Alfredo




On 2018-02-22 10:17, Alfredo E. Cardenas wrote:

Hi,
I am using gromacs to get the PMF of a peptide of  about 20 amino
acids, moving inside of a bilayer membrane. After pulling the peptide
inside the membrane now I am using  pull-coord1-type = umbrella
and pull-coord1-geometry  = distance to sample configurations in each
window for the umbrella simulations along the z axis (axis
perpendicular to the membrane surface). Runs finish ok, no error
messages. The problem is that when I looked at the contents of the
pullx file I observed spikes (up to 5 or more Angstroms) in the z
coordinate separating the center of mass of the peptide from the
membrane center. But when I extract the z coordinates of the center of
mass of the two groups and compute the difference the values look
reasonable with no spikes.

Here an example (it starts good):
time (ps)   from pullx  from traj analysis

   20.000  0.475923002  0.475919992
   200010.000  0.498394012  0.498389989
   200020.000  0.527589977  0.527589977
   200030.000  0.491834015  0.493739992
   200040.000  0.485377997  0.485379994
   200050.000  0.488474995  0.488469988
   200060.000  0.507991016  0.507990003
   200070.000  0.475095987  0.475100011
   200080.000  0.465889990  0.465889990
   200090.000  0.515878975  0.515879989
   200100.000  0.501435995  0.501429975
   200110.000  0.505191982  0.505190015

Here a bad section:

   214000.000  0.427343011  0.601450026
   214010.000  0.484564990  0.545799971
   214020.000  0.530139029  0.603110015
   214030.000  0.176231995  0.650319993
   214040.000  0.342045009  0.637109995
   214050.000  0.181202993  0.636659980
   214060.000  0.338808000  0.595300019
   214070.000  0.442301005  0.547529995
   214080.000  0.396046013  0.565050006
   214090.000  0.431407988  0.538460016
   214100.000  0.402586013  0.56825
   214110.000  0.438223004  0.575810015

Then good again:

   23.000  0.477869004  0.477869987
   230010.000  0.511840999  0.511839986
   230020.000  0.469146013  0.469150007
   230030.000  0.480194002  0.480190009
   230040.000  0.525618017  0.525619984
   230050.000  0.498955995  0.498950005
   230060.000  0.489230990  0.489230007
   230070.000  0.531931996  0.531930029
   230080.000  0.535376012  0.535380006
   230090.000  0.488822013  0.48883
   230100.000  0.510704994  0.510699987
   230110.000  0.524537981  0.524540007
   230120.000  0.513199985  0.513189971

This problem happens in most umbrella windows that I have examined,
sometimes several times during the long trajectories I am running. The
pullf output also have those spikes.

Here is the mdp file I am using:

integrator  = md
dt  = 0.002
nsteps  = 5000
nstlog  = 1
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy   = 500
nstenergy   = 500
;
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
;
tcoupl  = Nose-Hoover
tc_grps = PROT   MEMB   SOL_ION
tau_t   = 1.01.01.0
ref_t   = 303.15 303.15 303.15
;
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 500
comm_mode   = linear
comm_grps   = PROT_MEMB   SOL_ION
;
refcoord_scaling= com
;
pull= yes
pull-coord1-type= umbrella
pull-coord1-geometry= distance
pull-coord1-dim = N N Y
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= MEMB
pull-group2-name= PROT
pull-coord1-init= 0.400
pull-coord1-k

Re: [gmx-users] Potential energy coming out to be zero but not negative

2018-02-24 Thread Erik Marklund 
Dear Shayantani,

The output you quote show a negative potential energy. Is that not for the run 
you refer to?

(With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.)

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 23 Feb 2018, at 19:32, SHYANTANI MAITI 
mailto:shyantani.ma...@gmail.com>> wrote:

Hello Sir,

When I go for energy minimization for a protein complex containing 3
proteins, I obtain potential energy being minimized upto zero from
positive. The potential energy is not becoming negative even after running
for many steps as viewed in potential.xvg obtained after energy
minimzation.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you

--
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*Shyantani Maiti*
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Re: [gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

2018-02-24 Thread Erik Marklund 
Dear Cheng,

Gromacs is open source. Implement this at your own will. If there is a 
sufficient interest in such a feature it might even have a place in the 
official release at some point.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 22 Feb 2018, at 18:19, ZHANG Cheng 
<272699...@qq.com> wrote:

Dear Gromacs,
The scount.xvg file was obtained after running


echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map 
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg 
-tu ns


The secondary structures listed are:
'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix'


I ran the command for different proteins. It surprised me that the last 
'5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not 
have the '5-Helix', but why not just show them as 0? Can this be improved?


Because I am using a script to read the scount.xvg files, so I want all the 
files have the same format.


Thank you.


Yours sincerely
Cheng
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[gmx-users] tpr generation aborted

2018-02-24 Thread Mahmood Naderan 
Hi,
Following the Lusozume tutorial, I face an error at the step of generating 
ions.tpr which says too many warnings.

$ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -723452053
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 18409]:
  System has non-zero total charge: 8.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  



WARNING 1 [file topol.top, line 18409]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
  --- Thank You ---  

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   129    Protein residues
There are: 10644  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 69741.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.117 0.117 0.117
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 3 Mb of data

There were 2 notes

There was 1 warning

---
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.






Is it safe to use -maxwarn option?


Regards,
Mahmood
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Re: [gmx-users] installing error

2018-02-24 Thread Mark Abraham 
Hi,

Try getting a more up to date version from
http://manual.gromacs.org/documentation/ and follow the quick installation
guide there.

Mark

On Sat, Feb 24, 2018, 10:25 banijamali_fs  wrote:

> Hi there, I'm installing gromacs with these series of commands,
>
> sudo apt-get update
>
> sudo apt-get upgrade
>
> sudo apt-get install cmake
>
> cmake --version
>
> sudo apt-get install build-essential
>
> pwd
>
> cd Downloads/
>
> wget http://gerrit.gromacs.org/download/regressiontests-5.1.1.tar.gz
>
> tar xvzf regressiontests-5.1.1.tar.gz
>
> sudo apt-get install libfftw3-dev
>
> but when I want to run this " sudo apt-get install libfftw3-dev"
> command, I receive this error,
>
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package libfftw3-dev is not available, but is referred to by another
> package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> E: Package 'libfftw3-dev' has no installation candidate
>
> I don't know what should I do? please help me with my error
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Protein protein complex molecular dynamic simulation

2018-02-24 Thread SHYANTANI MAITI 
Can molecular dynamic simulation be performed over protein-protein
complexes using gromacs?
Thanking you,

-- 
Best regards,
*Shyantani Maiti*
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[gmx-users] Multiple runs for same system

2018-02-24 Thread Dr. Seema Mishra 
Hi, Can anyone tell me the steps and commands for performing multiple runs of 
50 ns for same protein-ligand system? Also the clustering for further analyses. 
Thanks. 
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[gmx-users] Protein protein complex md simulaton

2018-02-24 Thread SHYANTANI MAITI 
Dear all,
Does there exist any differences between the steps to follow for protein
and protein-protein complex md simulation?

-- 
Best regards,
*Shyantani Maiti*
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[gmx-users] installing error

2018-02-24 Thread banijamali_fs 
Hi there, I'm installing gromacs with these series of commands,

sudo apt-get update

sudo apt-get upgrade

sudo apt-get install cmake

cmake --version

sudo apt-get install build-essential

pwd

cd Downloads/

wget http://gerrit.gromacs.org/download/regressiontests-5.1.1.tar.gz

tar xvzf regressiontests-5.1.1.tar.gz

sudo apt-get install libfftw3-dev

but when I want to run this " sudo apt-get install libfftw3-dev"
command, I receive this error,

Reading package lists... Done
Building dependency tree 
Reading state information... Done
Package libfftw3-dev is not available, but is referred to by another
package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package 'libfftw3-dev' has no installation candidate

I don't know what should I do? please help me with my error
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