Re: [gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

I want to calculate water SDF around C-alpha of glycine molecule. So here i
have followed the commands..
Step 2:- gmx trjconv -s nptmd.tpr -f nptmd.xtc -o abc.tng -boxcenter tric
-ur compact -pbc none
and it asks me
Select group for output
Group 0 ( System) has  1543 elements
Group 1 ( Protein) has10 elements
Group 2 ( Protein-H) has 5 elements
Group 3 ( C-alpha) has 1 elements
Group 4 ( Backbone) has 3 elements
Group 5 ( MainChain) has 3 elements
Group 6 ( MainChain+Cb) has 3 elements
Group 7 ( MainChain+H) has 6 elements
Group 8 ( SideChain) has 4 elements
Group 9 ( SideChain-H) has 2 elements
Group10 (Prot-Masses) has10 elements
Group11 (non-Protein) has  1533 elements
Group12 ( Water) has  1533 elements
Group13 ( SOL) has  1533 elements
Group14 ( non-Water) has10 elements
and i have selected Group 0 (System),
Step3:- gmx trjconv -s nptmd.tpr -f abc.tng -o def.tng -fit rot+trans
Select group for least squares fit Group 0 ( System) has 1543 elements
Group 1 ( Protein) has 10 elements Group 2 ( Protein-H) has 5 elements
Group 3 ( C-alpha) has 1 elements Group 4 ( Backbone) has 3 elements Group
5 ( MainChain) has 3 elements Group 6 ( MainChain+Cb) has 3 elements Group
7 ( MainChain+H) has 6 elements Group 8 ( SideChain) has 4 elements Group 9
( SideChain-H) has 2 elements Group 10 ( Prot-Masses) has 10 elements Group
11 ( non-Protein) has 1533 elements Group 12 ( Water) has 1533 elements
Group 13 ( SOL) has 1533 elements Group 14 ( non-Water) has 10 elements
If i give group 3 (since it has C-alpha atoms), but i am getting an error as
Fatal error: Need at least 2 atoms to fit!

So, how can i solve this issue..?? since C-alpha is only one atom..

Thank you.


‌
 Sent with Mailtrack


On Tue, Apr 3, 2018 at 2:25 PM, Dilip H N  wrote:

> Hello,
> I want to do the Spatial Distribution Function,
> I tried to follow the manual gmx spatial.
> I am following the five-step protocol which is given in gmx spatial
> manual..
> 1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
> the Ow's of water molecules, Is this index good or should i have all the
> molecules..??)
> 2) in the second step-  "gmx trjconv -s a.tpr
>  -f a.tng
>  -o b.tng
>  -boxcenter tric -ur compact
> -pbc none" here we need to give the input file ie., -f a.tng from where
> does this .tng file i need to give the input..?? How do i create a .tng
> file.. what information does this tng file contain...??
>
> Any suggestions...
>
> Thank you.
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> ‌
>  Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Problems with Ionic Liquid Simulations

[Joshua Cummings]

Hi All,


I am currently trying to run a simulation on the ionic liquid 
1-butyl-3-methyl-imidazolium hexafluorophosphate ([Bmim][PF6]), but have run 
into a few errors I am unable to solve.


I've used the following steps in my simulation so far:


a) Generated the required .pdb files for both the [Bmim] cation and [PF6] anion.


b) Modified the following parameters in the OPLS-AA force field:

  *   atomtypes.atp
  *   aminoacids.rtp
  *   ffbonded.itp
  *   ffnonbonded.itp

 c)  Used Packmol to create a box containing a specific number of both the 
[Bmim] cations and [PF6] anions. This created the .pdb file [Bmim][PF6]



d) The generated .pdb file of the box from Packmol was then used with the 
pdb2gmx command to create the topol.top and .gro files.


e) Used the grompp command to assemble the structure, topology, and simulation 
parameters into a binary input file (.tpr) in order to be used for the energy 
minimisation. This was done via the following command:


gmx grompp -f minim.mdp -c bmimpf6_web_box.gro -p topol.top -o em.tpr


After inputting this command, the following errors were received:



WARNING 1 [file ffbonded.itp, line 2705]:
  Overriding Bond parameters.

  old: 0.1495 265266 0.1495 265266
  new: CSCT  10.15290   224200.0


WARNING 2 [file ffbonded.itp, line 2706]:
  Overriding Bond parameters.

  old: 0.1343 399154 0.1343 399154
  new: CRNA  10.13150   399200.0


WARNING 3 [file ffbonded.itp, line 2708]:
  Overriding Bond parameters.

  old: 0.1381 357314 0.1381 357314
  new: CWNA  10.13780   357400.0


WARNING 4 [file ffbonded.itp, line 2712]:
  Overriding Bond parameters.

  old: 0.109 284512 0.109 284512
  new: CTHC  10.10900   284500.0


WARNING 5 [file ffbonded.itp, line 2714]:
  Overriding Bond parameters.

  old: 0.1375 428442 0.1375 428442
  new: CWCW  10.13410   435200.0


WARNING 6 [file ffbonded.itp, line 2716]:
  Overriding Bond parameters.

  old: 0.108 307106 0.108 307106
  new: CRHA  10.10800   284500.0


WARNING 7 [file ffbonded.itp, line 2718]:
  Overriding Bond parameters.

  old: 0.108 307106 0.108 307106
  new: CWHA  10.10800   284500.0


WARNING 8 [file ffbonded.itp, line 2722]:
  Overriding Angle parameters.

  old: 120 585.76 120 585.76
  new: NA CR NA  1   109.800585.800


WARNING 9 [file ffbonded.itp, line 2727]:
  Overriding Angle parameters.

  old: 107.8 276.144 107.8 276.144
  new: HC CT HC  1   107.800276.100


WARNING 10 [file ffbonded.itp, line 2730]:
  Overriding Angle parameters.

  old: 109.8 585.76 109.8 585.76
  new: CR NA CW  1   108.000585.800


WARNING 11 [file ffbonded.itp, line 2733]:
  Overriding Angle parameters.

  old: 120 585.76 120 585.76
  new: CW CW NA  1   107.100585.800


WARNING 12 [file ffbonded.itp, line 2740]:
  Overriding Angle parameters.

  old: 120 292.88 120 292.88
  new: HA CR NA  1   125.100292.900


WARNING 13 [file ffbonded.itp, line 2741]:
  Overriding Angle parameters.

  old: 109.5 292.88 109.5 292.88
  new: CS CT HC  1   110.700313.800


WARNING 14 [file ffbonded.itp, line 2743]:
  Overriding Angle parameters.

  old: 121.6 292.88 121.6 292.88
  new: HA CW NA  1   122.000292.900


WARNING 15 [file ffbonded.itp, line 2755]:
  Overriding Ryckaert-Bell. parameters.

  old: 19.4556 0 -19.4556 0 0 0 19.4556 0 -19.4556 0 0 0
  new: HA CR NA CW  3  0.0  19.46000   0.0   
0.0   0.0   0.0


WARNING 16 [file ffbonded.itp, line 2756]:
  Overriding Ryckaert-Bell. parameters.

  old: 13.3888 0 -13.3888 0 0 0 13.3888 0 -13.3888 0 0 0
  new: HA CW NA CR  3  0.0  12.55000   0.0   
0.0   0.0   0.0


WARNING 17 [file ffbonded.itp, line 2765]:
  Overriding Ryckaert-Bell. parameters.

  old: 41.84 0 -41.84 0 0 0 41.84 0 -41.84 0 0 0
  new: NA CR NA CW  3  0.0  19.46000   0.0   
0.0   0.0   0.0


WARNING 18 [file ffbonded.itp, line 2772]:
  Overriding Ryckaert-Bell. parameters.

  old: 13.3888 0 -13.3888 0 0 0 13.3888 0 -13.3888 0 0 0
  new: CW CW NA CR  3  0.0  12.55000   0.0   
0.0   0.0   0.0

Generated 340725 of the 340725 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 340725 of the 340725 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Other_chain_A'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   500  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 23997.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
Estimate for the relative computational 

Re: [gmx-users] Perturbing Proteins

[Qasim Pars]

Hi,

Good question! The nstcomm is the frequency at which the center of mass motion 
is removed. My guess is that using short frequency for the nstcomm (e.g. 
nstcomm=1 while simulation time step is 1 fs, dt=0.001) can perturbe the 
system. That is, the system may not return to its starting/unperturbed state 
within a short time interval, while nstcomm is applied at every step on the 
system. Maybe Justin, Mark or the other developers/users can comment it better 
than me.

> On 3 Apr 2018, at 23:53, Sanyam Kapoor  wrote:
> 
> Hi all,
> 
> I was wondering if there is a principled way to perturb molecules and then
> see its energy converge to the stationary state via the simulation.
> Perturbation could mean changing the coordinates of the atoms, changing
> angles dihedrals etc. Anything related to the topology. I want to see this
> without the addition of any solvents in the environment.
> 
> My concern is that if I perturb randomly, the molecule may no more remain
> in a valid state (bad bond distance or bad angles/dihedrals etc.). Any
> ideas here?
> 
> Another question is that if I pick up any molecule from Protein DataBank
> and run a simulation without any solvent addition, does it converge further
> or are those molecules already on some minimum energy value attainable?
> 
> Please correct me if I miss some part of the molecular dynamics pipeline.
> -- 
> Regards,
> Sanyam Kapoor
> Masters in Computer Science
> Courant Institute, New York University
> https://www.sanyamkapoor.com
> -- 
> 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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Re: [gmx-users] gmx_mpi works in command line but not in script

[Alex]

Hi Marc,


On Tue, Apr 3, 2018 at 4:35 PM, Marc Hoemberger 
wrote:

> Hi Alex,
>
> I have had a similar issue on our cluster (different module files etc.) for
> me it turned out that on the actual compute nodes this module was not
> available. Thus if you run it from the command line on e.g. your login node
> you might have access to this compiler / modulefile, but when moving to a
> compute node it might not be there.
>

Yes, it think that is the reason. How did you solve it?

>
> Did you try running the command line invocation on the same node you are
> submitting the script to?
>
Actually, I can not find the list of node, otherwise I could log in inside
one of them (if I was allowed) to invoke gromacs there.

The rest of my run script is juts gmx_mpi grompp and mpirun gmx_mpi mdrun .

Best regards,
Alex

>
> -Marc
>
> On Tue, Apr 3, 2018 at 4:13 PM, Alex  wrote:
>
> > On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Tue, Apr 3, 2018 at 8:56 PM Alex  wrote:
> > >
> > > > Thanks Marc.
> > > >
> > > > I removed the two EXPORT line in the script but still missing the
> > library
> > > > (removing only the second line also did not help):
> > > >
> > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > > 'intel/composerxe/2015.1.133'
> > > >
> > >
> > > Why isn't this module being found?
> > >
> > I do not know. The funny point is that, the intel/composerxe/2015.1.133
> is
> > needed when I invoke gmx_mpi in command line, and after loading it, the
> > gmx_works fine. But I do not know why it can not be found inside script.
> >
> > >
> > >
> > > > 
> > > --
> > > > mpirun was unable to find the specified executable file, and
> therefore
> > > > did not launch the job.  This error was first reported for process
> > > > rank 0; it may have occurred for other processes as well.
> > > >
> > >
> > > If this was the error message, then you won't get a log file from the
> > > executable that wasn't found, so I presume that below you are looking
> at
> > an
> > > old log file...
> > >
> > > No, it can generate .log file, I ran it again and a new log file was
> > generated.
> >
> > >
> > > > And .log file:
> > > >
> > > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> > > cannot
> > > > open shared object file: No such file or directory
> > > >
> > >
> > > That's a library that has to come from the module that didn't load, so
> > look
> > > there.
> > >
> > >
> > Best regards,
> > Alex
> >
> >
> > > Mark
> > >
> > >
> > > > 
> > > --
> > > > mpirun was unable to find the specified executable file, and
> therefore
> > > > did not launch the job.  This error was first reported for process
> > > > rank 0; it may have occurred for other processes as well.
> > > >
> > > > Regards,
> > > > Alex
> > > >
> > > >
> > > > On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try
> > > letting
> > > > > the modules do it, since it is their job.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Tue, Apr 3, 2018, 20:29 Alex  wrote:
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > I have installed the gromacs2018.1 parallel in a cluster, it
> works
> > > > > > perfectly in the command line, of course after loading some
> module.
> > > > > > But when I put the commands along with loading module commands
> in a
> > > > bash
> > > > > > script to be submitted in the cluster, it crashes with the below
> > > > massage:
> > > > > >
> > > > > > ++
> > > > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile
> for
> > > > > > 'intel/composerxe/2015.1.133'
> > > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > > /home/alex23/.local/gromacs-2018.1/bin/../lib64/
> > libgromacs_mpi.so.3)
> > > > > >
> > > > > > And part of the log file:
> > > > > >
> > > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> > libgromacs_mpi.so.3)
> > > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> > libgromacs_mpi.so.3)
> > > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> > libgromacs_mpi.so.3)
> > > > > > gmx_mpi: error while loading shared 

[gmx-users] Perturbing Proteins

[Sanyam Kapoor]

Hi all,

I was wondering if there is a principled way to perturb molecules and then
see its energy converge to the stationary state via the simulation.
Perturbation could mean changing the coordinates of the atoms, changing
angles dihedrals etc. Anything related to the topology. I want to see this
without the addition of any solvents in the environment.

My concern is that if I perturb randomly, the molecule may no more remain
in a valid state (bad bond distance or bad angles/dihedrals etc.). Any
ideas here?

Another question is that if I pick up any molecule from Protein DataBank
and run a simulation without any solvent addition, does it converge further
or are those molecules already on some minimum energy value attainable?

Please correct me if I miss some part of the molecular dynamics pipeline.
-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com
-- 
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Re: [gmx-users] gmx_mpi works in command line but not in script

[Marc Hoemberger]

Hi Alex,

I have had a similar issue on our cluster (different module files etc.) for
me it turned out that on the actual compute nodes this module was not
available. Thus if you run it from the command line on e.g. your login node
you might have access to this compiler / modulefile, but when moving to a
compute node it might not be there.

Did you try running the command line invocation on the same node you are
submitting the script to?

-Marc

On Tue, Apr 3, 2018 at 4:13 PM, Alex  wrote:

> On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Tue, Apr 3, 2018 at 8:56 PM Alex  wrote:
> >
> > > Thanks Marc.
> > >
> > > I removed the two EXPORT line in the script but still missing the
> library
> > > (removing only the second line also did not help):
> > >
> > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > 'intel/composerxe/2015.1.133'
> > >
> >
> > Why isn't this module being found?
> >
> I do not know. The funny point is that, the intel/composerxe/2015.1.133 is
> needed when I invoke gmx_mpi in command line, and after loading it, the
> gmx_works fine. But I do not know why it can not be found inside script.
>
> >
> >
> > > 
> > --
> > > mpirun was unable to find the specified executable file, and therefore
> > > did not launch the job.  This error was first reported for process
> > > rank 0; it may have occurred for other processes as well.
> > >
> >
> > If this was the error message, then you won't get a log file from the
> > executable that wasn't found, so I presume that below you are looking at
> an
> > old log file...
> >
> > No, it can generate .log file, I ran it again and a new log file was
> generated.
>
> >
> > > And .log file:
> > >
> > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> > cannot
> > > open shared object file: No such file or directory
> > >
> >
> > That's a library that has to come from the module that didn't load, so
> look
> > there.
> >
> >
> Best regards,
> Alex
>
>
> > Mark
> >
> >
> > > 
> > --
> > > mpirun was unable to find the specified executable file, and therefore
> > > did not launch the job.  This error was first reported for process
> > > rank 0; it may have occurred for other processes as well.
> > >
> > > Regards,
> > > Alex
> > >
> > >
> > > On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try
> > letting
> > > > the modules do it, since it is their job.
> > > >
> > > > Mark
> > > >
> > > > On Tue, Apr 3, 2018, 20:29 Alex  wrote:
> > > >
> > > > > Dear all,
> > > > >
> > > > > I have installed the gromacs2018.1 parallel in a cluster, it works
> > > > > perfectly in the command line, of course after loading some module.
> > > > > But when I put the commands along with loading module commands in a
> > > bash
> > > > > script to be submitted in the cluster, it crashes with the below
> > > massage:
> > > > >
> > > > > ++
> > > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > > > 'intel/composerxe/2015.1.133'
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > /home/alex23/.local/gromacs-2018.1/bin/../lib64/
> libgromacs_mpi.so.3)
> > > > >
> > > > > And part of the log file:
> > > > >
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> libgromacs_mpi.so.3)
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> libgromacs_mpi.so.3)
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/
> libgromacs_mpi.so.3)
> > > > > gmx_mpi: error while loading shared libraries:
> libmkl_intel_lp64.so:
> > > > cannot
> > > > > open shared object file: No such file or directory
> > > > > ++
> > > > >
> > > > > Here is part of my script.sh file
> > > > > ++
> > > > > . /etc/profile.d/modules.sh
> > > > > module load intel/composerxe/2015.1.133
> > > > > module load shared
> > > > > module load clusterA
> > > > > module load gcc/4.8.1
> > > > > module load sge/univa
> > > > > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> > > > > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> > > > > export
> > > > >
> > > > > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_
> > > > 

Re: [gmx-users] gmx_mpi works in command line but not in script

[Mark Abraham]

Hi,

I can't help you troubleshoot your use of your cluster's modules (nor guess
about what's in the rest of your run script). Talk to the people paid to do
it ;-)

Mark

On Tue, Apr 3, 2018 at 10:15 PM Alex  wrote:

> On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Tue, Apr 3, 2018 at 8:56 PM Alex  wrote:
> >
> > > Thanks Marc.
> > >
> > > I removed the two EXPORT line in the script but still missing the
> library
> > > (removing only the second line also did not help):
> > >
> > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > 'intel/composerxe/2015.1.133'
> > >
> >
> > Why isn't this module being found?
> >
> I do not know. The funny point is that, the intel/composerxe/2015.1.133 is
> needed when I invoke gmx_mpi in command line, and after loading it, the
> gmx_works fine. But I do not know why it can not be found inside script.
>
> >
> >
> > > 
> > --
> > > mpirun was unable to find the specified executable file, and therefore
> > > did not launch the job.  This error was first reported for process
> > > rank 0; it may have occurred for other processes as well.
> > >
> >
> > If this was the error message, then you won't get a log file from the
> > executable that wasn't found, so I presume that below you are looking at
> an
> > old log file...
> >
> > No, it can generate .log file, I ran it again and a new log file was
> generated.
>
> >
> > > And .log file:
> > >
> > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> > cannot
> > > open shared object file: No such file or directory
> > >
> >
> > That's a library that has to come from the module that didn't load, so
> look
> > there.
> >
> >
> Best regards,
> Alex
>
>
> > Mark
> >
> >
> > > 
> > --
> > > mpirun was unable to find the specified executable file, and therefore
> > > did not launch the job.  This error was first reported for process
> > > rank 0; it may have occurred for other processes as well.
> > >
> > > Regards,
> > > Alex
> > >
> > >
> > > On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try
> > letting
> > > > the modules do it, since it is their job.
> > > >
> > > > Mark
> > > >
> > > > On Tue, Apr 3, 2018, 20:29 Alex  wrote:
> > > >
> > > > > Dear all,
> > > > >
> > > > > I have installed the gromacs2018.1 parallel in a cluster, it works
> > > > > perfectly in the command line, of course after loading some module.
> > > > > But when I put the commands along with loading module commands in a
> > > bash
> > > > > script to be submitted in the cluster, it crashes with the below
> > > massage:
> > > > >
> > > > > ++
> > > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > > > 'intel/composerxe/2015.1.133'
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > >
> /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > >
> > > > > And part of the log file:
> > > > >
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > >
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > >
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > > `GLIBCXX_3.4.20' not found (required by
> > > > >
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > > gmx_mpi: error while loading shared libraries:
> libmkl_intel_lp64.so:
> > > > cannot
> > > > > open shared object file: No such file or directory
> > > > > ++
> > > > >
> > > > > Here is part of my script.sh file
> > > > > ++
> > > > > . /etc/profile.d/modules.sh
> > > > > module load intel/composerxe/2015.1.133
> > > > > module load shared
> > > > > module load clusterA
> > > > > module load gcc/4.8.1
> > > > > module load sge/univa
> > > > > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> > > > > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> > > > > export
> > > > >
> > > > > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_
> > > > LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> > > > > 
> > > > >
> > > > > Do you know what I am missing?
> > > > > Thanks
> > > > > Alex
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > 

Re: [gmx-users] gmx_mpi works in command line but not in script

[Alex]

On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, Apr 3, 2018 at 8:56 PM Alex  wrote:
>
> > Thanks Marc.
> >
> > I removed the two EXPORT line in the script but still missing the library
> > (removing only the second line also did not help):
> >
> > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > 'intel/composerxe/2015.1.133'
> >
>
> Why isn't this module being found?
>
I do not know. The funny point is that, the intel/composerxe/2015.1.133 is
needed when I invoke gmx_mpi in command line, and after loading it, the
gmx_works fine. But I do not know why it can not be found inside script.

>
>
> > 
> --
> > mpirun was unable to find the specified executable file, and therefore
> > did not launch the job.  This error was first reported for process
> > rank 0; it may have occurred for other processes as well.
> >
>
> If this was the error message, then you won't get a log file from the
> executable that wasn't found, so I presume that below you are looking at an
> old log file...
>
> No, it can generate .log file, I ran it again and a new log file was
generated.

>
> > And .log file:
> >
> > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> cannot
> > open shared object file: No such file or directory
> >
>
> That's a library that has to come from the module that didn't load, so look
> there.
>
>
Best regards,
Alex


> Mark
>
>
> > 
> --
> > mpirun was unable to find the specified executable file, and therefore
> > did not launch the job.  This error was first reported for process
> > rank 0; it may have occurred for other processes as well.
> >
> > Regards,
> > Alex
> >
> >
> > On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try
> letting
> > > the modules do it, since it is their job.
> > >
> > > Mark
> > >
> > > On Tue, Apr 3, 2018, 20:29 Alex  wrote:
> > >
> > > > Dear all,
> > > >
> > > > I have installed the gromacs2018.1 parallel in a cluster, it works
> > > > perfectly in the command line, of course after loading some module.
> > > > But when I put the commands along with loading module commands in a
> > bash
> > > > script to be submitted in the cluster, it crashes with the below
> > massage:
> > > >
> > > > ++
> > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > > 'intel/composerxe/2015.1.133'
> > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > `GLIBCXX_3.4.20' not found (required by
> > > > /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > >
> > > > And part of the log file:
> > > >
> > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > `GLIBCXX_3.4.20' not found (required by
> > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > `GLIBCXX_3.4.20' not found (required by
> > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > > `GLIBCXX_3.4.20' not found (required by
> > > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> > > cannot
> > > > open shared object file: No such file or directory
> > > > ++
> > > >
> > > > Here is part of my script.sh file
> > > > ++
> > > > . /etc/profile.d/modules.sh
> > > > module load intel/composerxe/2015.1.133
> > > > module load shared
> > > > module load clusterA
> > > > module load gcc/4.8.1
> > > > module load sge/univa
> > > > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> > > > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> > > > export
> > > >
> > > > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_
> > > LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> > > > 
> > > >
> > > > Do you know what I am missing?
> > > > Thanks
> > > > Alex
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read 

Re: [gmx-users] gmx_mpi works in command line but not in script

[Mark Abraham]

Hi,

On Tue, Apr 3, 2018 at 8:56 PM Alex  wrote:

> Thanks Marc.
>
> I removed the two EXPORT line in the script but still missing the library
> (removing only the second line also did not help):
>
> ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> 'intel/composerxe/2015.1.133'
>

Why isn't this module being found?


> --
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
>

If this was the error message, then you won't get a log file from the
executable that wasn't found, so I presume that below you are looking at an
old log file...


> And .log file:
>
> gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
> open shared object file: No such file or directory
>

That's a library that has to come from the module that didn't load, so look
there.

Mark


> --
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
>
> Regards,
> Alex
>
>
> On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting
> > the modules do it, since it is their job.
> >
> > Mark
> >
> > On Tue, Apr 3, 2018, 20:29 Alex  wrote:
> >
> > > Dear all,
> > >
> > > I have installed the gromacs2018.1 parallel in a cluster, it works
> > > perfectly in the command line, of course after loading some module.
> > > But when I put the commands along with loading module commands in a
> bash
> > > script to be submitted in the cluster, it crashes with the below
> massage:
> > >
> > > ++
> > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > > 'intel/composerxe/2015.1.133'
> > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > `GLIBCXX_3.4.20' not found (required by
> > > /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > >
> > > And part of the log file:
> > >
> > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > `GLIBCXX_3.4.20' not found (required by
> > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > `GLIBCXX_3.4.20' not found (required by
> > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > > `GLIBCXX_3.4.20' not found (required by
> > > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> > cannot
> > > open shared object file: No such file or directory
> > > ++
> > >
> > > Here is part of my script.sh file
> > > ++
> > > . /etc/profile.d/modules.sh
> > > module load intel/composerxe/2015.1.133
> > > module load shared
> > > module load clusterA
> > > module load gcc/4.8.1
> > > module load sge/univa
> > > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> > > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> > > export
> > >
> > > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_
> > LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> > > 
> > >
> > > Do you know what I am missing?
> > > Thanks
> > > Alex
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
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* Please search the archive at 

Re: [gmx-users] gmx_mpi works in command line but not in script

[Alex]

Thanks Marc.

I removed the two EXPORT line in the script but still missing the library
(removing only the second line also did not help):

ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
'intel/composerxe/2015.1.133'
--
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

And .log file:

gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
open shared object file: No such file or directory
--
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

Regards,
Alex


On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham 
wrote:

> Hi,
>
> It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting
> the modules do it, since it is their job.
>
> Mark
>
> On Tue, Apr 3, 2018, 20:29 Alex  wrote:
>
> > Dear all,
> >
> > I have installed the gromacs2018.1 parallel in a cluster, it works
> > perfectly in the command line, of course after loading some module.
> > But when I put the commands along with loading module commands in a bash
> > script to be submitted in the cluster, it crashes with the below massage:
> >
> > ++
> > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> > 'intel/composerxe/2015.1.133'
> > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > `GLIBCXX_3.4.20' not found (required by
> > /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> >
> > And part of the log file:
> >
> > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > `GLIBCXX_3.4.20' not found (required by
> > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > `GLIBCXX_3.4.20' not found (required by
> > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> > `GLIBCXX_3.4.20' not found (required by
> > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so:
> cannot
> > open shared object file: No such file or directory
> > ++
> >
> > Here is part of my script.sh file
> > ++
> > . /etc/profile.d/modules.sh
> > module load intel/composerxe/2015.1.133
> > module load shared
> > module load clusterA
> > module load gcc/4.8.1
> > module load sge/univa
> > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> > export
> >
> > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_
> LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> > 
> >
> > Do you know what I am missing?
> > Thanks
> > Alex
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] gmx_mpi works in command line but not in script

[Mark Abraham]

Hi,

It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting
the modules do it, since it is their job.

Mark

On Tue, Apr 3, 2018, 20:29 Alex  wrote:

> Dear all,
>
> I have installed the gromacs2018.1 parallel in a cluster, it works
> perfectly in the command line, of course after loading some module.
> But when I put the commands along with loading module commands in a bash
> script to be submitted in the cluster, it crashes with the below massage:
>
> ++
> ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> 'intel/composerxe/2015.1.133'
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
>
> And part of the log file:
>
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
> open shared object file: No such file or directory
> ++
>
> Here is part of my script.sh file
> ++
> . /etc/profile.d/modules.sh
> module load intel/composerxe/2015.1.133
> module load shared
> module load clusterA
> module load gcc/4.8.1
> module load sge/univa
> module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> export
>
> LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> 
>
> Do you know what I am missing?
> Thanks
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Performance

[Szilárd Páll]

Hi,

Your system is exploding, some atoms end up with coordinates of around
10^9 which then throw off the PBC code that tries to put atoms back in
the box. This will normally not happen as constraining will already
fail with such huge coordinates, I think, so technically it is a bug,
we could handle this corner-case better.

However, if you need to verify your system setup as it is unstable
(not well equilibrated or the time-step too long).

--
Szilárd


On Thu, Mar 29, 2018 at 3:50 PM, Myunggi Yi  wrote:
> Dear Szilard,
>
> Can you run this simulation?
>
> Simulation doesn't crush and doesn't generate error message.
> It take forever without updating report in log file or other output files.
>
> Is this a bug?
>
>
>
> On Thu, Mar 29, 2018 at 7:58 AM, Szilárd Páll 
> wrote:
>
>> Thanks. Looks like the messages and error handling is somewhat
>> confusing; you must have the OMP_NUM_THREADS environment variable set
>> which (just as setting -ntomp), without setting -ntmpi too is not
>> supported.
>>
>> Either let mdrun decide about the thread count or set -ntmpi manually.
>>
>> --
>> Szilárd
>>
>>
>> On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi  wrote:
>> > Does it work?
>> >
>> > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl
>> >
>> > How about this?
>> >
>> >
>> > Myunggi Yi
>> >
>> > On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham > >
>> > wrote:
>> >
>> >> Hi,
>> >>
>> >> Attachments can't be accepted on the list - please upload to a file
>> sharing
>> >> service and share links to those.
>> >>
>> >> Mark
>> >>
>> >> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi 
>> wrote:
>> >>
>> >> > I am attaching the file.
>> >> >
>> >> > Thank you.
>> >> >
>> >> > Myunggi Yi
>> >> >
>> >> > On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll <
>> pall.szil...@gmail.com>
>> >> > wrote:
>> >> >
>> >> > > Again, please share the exact log files / description of inputs.
>> What
>> >> > > does "bad performance" mean?
>> >> > > --
>> >> > > Szilárd
>> >> > >
>> >> > >
>> >> > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi 
>> >> > wrote:
>> >> > > > Dear users,
>> >> > > >
>> >> > > > I have two questions.
>> >> > > >
>> >> > > >
>> >> > > > 1. I used to run typical simulations with the following command.
>> >> > > >
>> >> > > > gmx mdrun -deffnm md
>> >> > > >
>> >> > > > I had no problem.
>> >> > > >
>> >> > > >
>> >> > > > Now I am running a simulation with "Dry_Martini" FF with the
>> >> following
>> >> > > > input.
>> >> > > >
>> >> > > >
>> >> > > > integrator   = sd
>> >> > > > tinit= 0.0
>> >> > > > dt   = 0.040
>> >> > > > nsteps   = 100
>> >> > > >
>> >> > > > nstlog   = 5000
>> >> > > > nstenergy= 5000
>> >> > > > nstxout-compressed   = 5000
>> >> > > > compressed-x-precision   = 100
>> >> > > >
>> >> > > > cutoff-scheme= Verlet
>> >> > > > nstlist  = 10
>> >> > > > ns_type  = grid
>> >> > > > pbc  = xyz
>> >> > > > verlet-buffer-tolerance  = 0.005
>> >> > > >
>> >> > > > epsilon_r= 15
>> >> > > > coulombtype  = reaction-field
>> >> > > > rcoulomb = 1.1
>> >> > > > vdw_type = cutoff
>> >> > > > vdw-modifier = Potential-shift-verlet
>> >> > > > rvdw = 1.1
>> >> > > >
>> >> > > > tc-grps  = system
>> >> > > > tau_t= 4.0
>> >> > > > ref_t= 310
>> >> > > >
>> >> > > > ; Pressure coupling:
>> >> > > > Pcoupl   = no
>> >> > > >
>> >> > > > ; GENERATE VELOCITIES FOR STARTUP RUN:
>> >> > > > gen_vel  = yes
>> >> > > > gen_temp = 310
>> >> > > > gen_seed = 1521731368
>> >> > > >
>> >> > > >
>> >> > > >
>> >> > > > If I use the same command to submit the job.
>> >> > > > I got the following error. I don't know why.
>> >> > > >
>> >> > > > ---
>> >> > > > Program: gmx mdrun, version 2018.1
>> >> > > > Source file: src/gromacs/taskassignment/resourcedivision.cpp
>> (line
>> >> 224)
>> >> > > >
>> >> > > > Fatal error:
>> >> > > > When using GPUs, setting the number of OpenMP threads without
>> >> > specifying
>> >> > > the
>> >> > > > number of ranks can lead to conflicting demands. Please specify
>> the
>> >> > > number
>> >> > > > of
>> >> > > > thread-MPI ranks as well (option -ntmpi).
>> >> > > >
>> >> > > > For more information and tips for troubleshooting, please check
>> the
>> >> > > GROMACS
>> >> > > > website at http://www.gromacs.org/Documentation/Errors
>> >> > > > ---
>> >> > > >
>> >> > > >
>> >> > > > So I did run simulation with the following command.
>> >> > > >
>> >> > > 

[gmx-users] gmx_mpi works in command line but not in script

[Alex]

Dear all,

I have installed the gromacs2018.1 parallel in a cluster, it works
perfectly in the command line, of course after loading some module.
But when I put the commands along with loading module commands in a bash
script to be submitted in the cluster, it crashes with the below massage:

++
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
'intel/composerxe/2015.1.133'
gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
`GLIBCXX_3.4.20' not found (required by
/home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)

And part of the log file:

gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
`GLIBCXX_3.4.20' not found (required by
/home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
`GLIBCXX_3.4.20' not found (required by
/home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
`GLIBCXX_3.4.20' not found (required by
/home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
open shared object file: No such file or directory
++

Here is part of my script.sh file
++
. /etc/profile.d/modules.sh
module load intel/composerxe/2015.1.133
module load shared
module load clusterA
module load gcc/4.8.1
module load sge/univa
module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
export
LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}


Do you know what I am missing?
Thanks
Alex
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Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

[Szilárd Páll]

On Tue, Apr 3, 2018 at 5:10 PM, Jochen Hub  wrote:
>
>
> Am 03.04.18 um 16:26 schrieb Szilárd Páll:
>
>> On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub  wrote:
>>>
>>>benchmar
>>>
>>> Am 29.03.18 um 20:57 schrieb Szilárd Páll:
>>>
 Hi Jochen,

 For that particular benchmark I only measured performance with
 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
 to do the runs on all possible core counts with increments of 1, but
 that won't tell a whole lot more than what the performance is of a run
 using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
 extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
 good estimate is tricky (given that the latter has 25% more cores for
 the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
 chips which have different performance characteristics.

 As Mark notes, there are some mdp option as well as some system
 charateristics that will have a strong influence on performance -- if
 tens of % is something you consider "strong" (some users are fine to
 be within a 2x ballpark :).

 What's worth considering is to try to avoid ending up strongly CPU or
 GPU bound from start. That may admittedly could be a difficult task
 you would run e.g. both biased MD with large pull groups and all-bonds
 constraints with Amber FF on large-ish (>100k) systems as well as
 vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
 hardware the former will be more prone to be CPU-bound while the
 latter will have relatively more GPU-heavy workload.

 There are many factors that influence the performance of a run and
 therefore giving a the one right answer to your question is not really
 possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
 generally sufficient for "typical" protein simulations to run at >=85%
 of peak.
>>>
>>>
>>>
>>> Hi Szilárd,
>>>
>>> many thanks, this alrady helps me a lot. Just to get it 100% clear what
>>> you
>>> mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22
>>> core-GHz,
>>> right?
>>
>>
>> Yes, that's what I was referring to; note that a 2630v4 won't be
>> running at a 2.2 GHz base clock if you run AVX code ;)
>
>
> Okay, I didn't know this. What would be the base clock instead with AVX
> code?


Short version: It's not easy to out details as Intel conveniently
omits it from the specs, but it's AFAIK 3-400 MHz lower; also note
that "turbo bins" change as a function of cores used (so you can't
just benchmark on a few cores leaving the rest idle). Also, the actual
clock speed (and overall performance) depend on other factors too so
benchmarking and extrapolation might require consider other factors
too.

Let me know if you are interested in more details.

--
Szilárd

>
>>
>>> Thanks,
>>> Jochen
>>>
>>>

 Cheers,
 --
 Szilárd


 On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham 
 wrote:
>
>
> Hi,
>
> On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub  wrote:
>
>> Dear Gromacs community, dear Mark,
>>
>> Mark showed in the webinar today that having more than 8 Xeon
>> E5-26XXv4
>> cores does not help when using a GTX 1080Ti and PME on the GPU.
>>
>
> ... for that particular simulation system.
>
>
>> Unfortunately, there were no data points between 4 and 8 CPU cores,
>> hence it was not clear at which #cores the performance actually levels
>> off. With a GTX 1080 (not Ti) I once found that having more than 5
>> Xeon
>> cores does not help, if not having UB potentials, but I don't have a
>> 1080Ti at hand to test for that.
>>
>
> Those data points may not have been run. Szilard might have the data -
> this
> was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he
> shared.
>
>
>> So my questions are:
>>
>> - At which number of E5-26XXv4 cores does the performance for common
>> systems level off with a 1080Ti for your test system (GLIC)?
>>
>> - Does the answer depend strongly on the mdp settings (in particular
>> on
>> the LJ cutoff)?
>>
>
> Longer LJ cutoff (e.g. from different forcefields) will certainly
> require
> more non-bonded work, so then fewer CPU cores would be needed to do the
> remaining non-offloaded work. However any sweet spot for a particular
> .tpr
> would be highly dependent on other effects, such as the ratio of
> solvent
> (which typically has less LJ and simpler update) to solute, or the
> density
> of dihedral or U-B interactions. And doing pulling or FEP is very
> different
> again. The sweet spot for the next project will be elsewhere, sadly.
>
> This would help us a lot when choosing the appropriate CPU for a

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

[Jochen Hub]

Am 03.04.18 um 16:26 schrieb Szilárd Páll:

On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub  wrote:



Am 29.03.18 um 20:57 schrieb Szilárd Páll:


Hi Jochen,

For that particular benchmark I only measured performance with
1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
to do the runs on all possible core counts with increments of 1, but
that won't tell a whole lot more than what the performance is of a run
using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
good estimate is tricky (given that the latter has 25% more cores for
the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
chips which have different performance characteristics.

As Mark notes, there are some mdp option as well as some system
charateristics that will have a strong influence on performance -- if
tens of % is something you consider "strong" (some users are fine to
be within a 2x ballpark :).

What's worth considering is to try to avoid ending up strongly CPU or
GPU bound from start. That may admittedly could be a difficult task
you would run e.g. both biased MD with large pull groups and all-bonds
constraints with Amber FF on large-ish (>100k) systems as well as
vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
hardware the former will be more prone to be CPU-bound while the
latter will have relatively more GPU-heavy workload.

There are many factors that influence the performance of a run and
therefore giving a the one right answer to your question is not really
possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
generally sufficient for "typical" protein simulations to run at >=85%
of peak.



Hi Szilárd,

many thanks, this alrady helps me a lot. Just to get it 100% clear what you
mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz,
right?


Yes, that's what I was referring to; note that a 2630v4 won't be
running at a 2.2 GHz base clock if you run AVX code ;)


Okay, I didn't know this. What would be the base clock instead with AVX 
code?





Thanks,
Jochen




Cheers,
--
Szilárd


On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham 
wrote:


Hi,

On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub  wrote:


Dear Gromacs community, dear Mark,

Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
cores does not help when using a GTX 1080Ti and PME on the GPU.



... for that particular simulation system.



Unfortunately, there were no data points between 4 and 8 CPU cores,
hence it was not clear at which #cores the performance actually levels
off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
cores does not help, if not having UB potentials, but I don't have a
1080Ti at hand to test for that.



Those data points may not have been run. Szilard might have the data -
this
was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.



So my questions are:

- At which number of E5-26XXv4 cores does the performance for common
systems level off with a 1080Ti for your test system (GLIC)?

- Does the answer depend strongly on the mdp settings (in particular on
the LJ cutoff)?



Longer LJ cutoff (e.g. from different forcefields) will certainly require
more non-bonded work, so then fewer CPU cores would be needed to do the
remaining non-offloaded work. However any sweet spot for a particular
.tpr
would be highly dependent on other effects, such as the ratio of solvent
(which typically has less LJ and simpler update) to solute, or the
density
of dihedral or U-B interactions. And doing pulling or FEP is very
different
again. The sweet spot for the next project will be elsewhere, sadly.

This would help us a lot when choosing the appropriate CPU for a 1080Ti.



Many thanks for any suggestions,
Jochen

--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany


.
Phone: +49-551-39-14189 <+49%20551%203914189>
http://cmb.bio.uni-goettingen.de/
---
--
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posting!

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Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

[Szilárd Páll]

On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub  wrote:
>
>
> Am 29.03.18 um 20:57 schrieb Szilárd Páll:
>
>> Hi Jochen,
>>
>> For that particular benchmark I only measured performance with
>> 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
>> to do the runs on all possible core counts with increments of 1, but
>> that won't tell a whole lot more than what the performance is of a run
>> using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
>> extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
>> good estimate is tricky (given that the latter has 25% more cores for
>> the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
>> chips which have different performance characteristics.
>>
>> As Mark notes, there are some mdp option as well as some system
>> charateristics that will have a strong influence on performance -- if
>> tens of % is something you consider "strong" (some users are fine to
>> be within a 2x ballpark :).
>>
>> What's worth considering is to try to avoid ending up strongly CPU or
>> GPU bound from start. That may admittedly could be a difficult task
>> you would run e.g. both biased MD with large pull groups and all-bonds
>> constraints with Amber FF on large-ish (>100k) systems as well as
>> vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
>> hardware the former will be more prone to be CPU-bound while the
>> latter will have relatively more GPU-heavy workload.
>>
>> There are many factors that influence the performance of a run and
>> therefore giving a the one right answer to your question is not really
>> possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
>> generally sufficient for "typical" protein simulations to run at >=85%
>> of peak.
>
>
> Hi Szilárd,
>
> many thanks, this alrady helps me a lot. Just to get it 100% clear what you
> mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz,
> right?

Yes, that's what I was referring to; note that a 2630v4 won't be
running at a 2.2 GHz base clock if you run AVX code ;)

> Thanks,
> Jochen
>
>
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham 
>> wrote:
>>>
>>> Hi,
>>>
>>> On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub  wrote:
>>>
 Dear Gromacs community, dear Mark,

 Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
 cores does not help when using a GTX 1080Ti and PME on the GPU.

>>>
>>> ... for that particular simulation system.
>>>
>>>
 Unfortunately, there were no data points between 4 and 8 CPU cores,
 hence it was not clear at which #cores the performance actually levels
 off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
 cores does not help, if not having UB potentials, but I don't have a
 1080Ti at hand to test for that.

>>>
>>> Those data points may not have been run. Szilard might have the data -
>>> this
>>> was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.
>>>
>>>
 So my questions are:

 - At which number of E5-26XXv4 cores does the performance for common
 systems level off with a 1080Ti for your test system (GLIC)?

 - Does the answer depend strongly on the mdp settings (in particular on
 the LJ cutoff)?

>>>
>>> Longer LJ cutoff (e.g. from different forcefields) will certainly require
>>> more non-bonded work, so then fewer CPU cores would be needed to do the
>>> remaining non-offloaded work. However any sweet spot for a particular
>>> .tpr
>>> would be highly dependent on other effects, such as the ratio of solvent
>>> (which typically has less LJ and simpler update) to solute, or the
>>> density
>>> of dihedral or U-B interactions. And doing pulling or FEP is very
>>> different
>>> again. The sweet spot for the next project will be elsewhere, sadly.
>>>
>>> This would help us a lot when choosing the appropriate CPU for a 1080Ti.


 Many thanks for any suggestions,
 Jochen

 --
 ---
 Dr. Jochen Hub
 Computational Molecular Biophysics Group
 Institute for Microbiology and Genetics
 Georg-August-University of Göttingen
 Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany

 
 .
 Phone: +49-551-39-14189 <+49%20551%203914189>
 http://cmb.bio.uni-goettingen.de/
 ---
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

[Jochen Hub]

Am 29.03.18 um 20:57 schrieb Szilárd Páll:

Hi Jochen,

For that particular benchmark I only measured performance with
1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
to do the runs on all possible core counts with increments of 1, but
that won't tell a whole lot more than what the performance is of a run
using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
good estimate is tricky (given that the latter has 25% more cores for
the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
chips which have different performance characteristics.

As Mark notes, there are some mdp option as well as some system
charateristics that will have a strong influence on performance -- if
tens of % is something you consider "strong" (some users are fine to
be within a 2x ballpark :).

What's worth considering is to try to avoid ending up strongly CPU or
GPU bound from start. That may admittedly could be a difficult task
you would run e.g. both biased MD with large pull groups and all-bonds
constraints with Amber FF on large-ish (>100k) systems as well as
vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
hardware the former will be more prone to be CPU-bound while the
latter will have relatively more GPU-heavy workload.

There are many factors that influence the performance of a run and
therefore giving a the one right answer to your question is not really
possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
generally sufficient for "typical" protein simulations to run at >=85%
of peak.


Hi Szilárd,

many thanks, this alrady helps me a lot. Just to get it 100% clear what 
you mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 
core-GHz, right?


Thanks,
Jochen



Cheers,
--
Szilárd


On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham  wrote:

Hi,

On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub  wrote:


Dear Gromacs community, dear Mark,

Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
cores does not help when using a GTX 1080Ti and PME on the GPU.



... for that particular simulation system.



Unfortunately, there were no data points between 4 and 8 CPU cores,
hence it was not clear at which #cores the performance actually levels
off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
cores does not help, if not having UB potentials, but I don't have a
1080Ti at hand to test for that.



Those data points may not have been run. Szilard might have the data - this
was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.



So my questions are:

- At which number of E5-26XXv4 cores does the performance for common
systems level off with a 1080Ti for your test system (GLIC)?

- Does the answer depend strongly on the mdp settings (in particular on
the LJ cutoff)?



Longer LJ cutoff (e.g. from different forcefields) will certainly require
more non-bonded work, so then fewer CPU cores would be needed to do the
remaining non-offloaded work. However any sweet spot for a particular .tpr
would be highly dependent on other effects, such as the ratio of solvent
(which typically has less LJ and simpler update) to solute, or the density
of dihedral or U-B interactions. And doing pulling or FEP is very different
again. The sweet spot for the next project will be elsewhere, sadly.

This would help us a lot when choosing the appropriate CPU for a 1080Ti.


Many thanks for any suggestions,
Jochen

--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany

.
Phone: +49-551-39-14189 <+49%20551%203914189>
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, 

Re: [gmx-users] error in index file

[Justin Lemkul]

On 4/3/18 5:50 AM, Joe Jordan wrote:

Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.


Neither gmx select nor gmx make_ndx should be necessary here. All 
defined [moleculetypes] are default index groups. The ligand should show 
up as a choice from any GROMACS program without needing an index file at 
all.


-Justin


On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal 
wrote:


I'm using v4.6.2

$make_ndx -f npt.gro


r 306 (residue num of ligand)
name 24 Ligand

This should do the work right ?

On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:


I got a group with the right number of atoms when I tried it. What

version

of gromacs are you using and what selection string are you using?

On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
wrote:


Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-
L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 

wrote:

Can you post the gro file and the resulting index file?

On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <

abhisek.m...@gmail.com>

wrote:


Hi,

I'm just having some issue creating index file for umbrella

sampling.

I have a ligand:
Group20 (NAP) has73 elements

Now when I run following command:
gmx make_ndx -f npt.gro

and try to add NAP for index.ndx, only 6 elements were being added.

I don't understand the problem here.

NAP is clearly showing is of 73 elements, but how come it is

showing

me 6

elements when added to index file ?

Please help me out here.

Thanks.

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

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Re: [gmx-users] Possible to extract gro file from a tpr?

[Mark Abraham]

Hi,

As Justin observed, editconf -f your.tpr -o your.pdb just works.

Mark
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Mark Abraham]

We haven't yet moved to Discourse ;-)

On Tue, Apr 3, 2018, 10:54 Viveca Lindahl  wrote:

> Wish I could +1 the best response here :) Thanks.
>
> --
> Viveca
>
>
> On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham 
> wrote:
>
> > Just say No! :-)
> >
> > On Fri, Mar 30, 2018, 19:58 Alex  wrote:
> >
> > > Or, and that is a very peculiar option, genion with -conc 0. :)
> > >
> > > Alex
> > >
> > >
> > > On 3/30/2018 4:28 AM, Justin Lemkul wrote:
> > > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl <
> > vivecalind...@gmail.com>
> > > > wrote:
> > > >
> > > >> Hi users,
> > > >>
> > > >> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx
> > > mdrun
> > > >> -nsteps 0' does not give a confout.gro :)
> > > >>
> > > > Just use editconf.
> > > >
> > > > -Justin
> > > >
> > > >
> > > >> --
> > > >> Viveca
> > > >> --
> > > >> Gromacs Users mailing list
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Re: [gmx-users] Compute average forces along a trajectory

[Simone Orioli]

Dear Mark,
Thanks. I did not specify that parameter, as you correctly suggested. I'm
re-running the simulations and see what happens.

Thanks
Simone

Il lun 2 apr 2018, 17:44 Mark Abraham  ha scritto:

> Hi,
>
> Probably you didn't use nstfout to save forces - use gmx check -f on your
> trajectory file to see.
>
> Mark
>
> On Mon, Apr 2, 2018, 15:55 Simone Orioli  wrote:
>
> > Dear all,
> > I have a short simulation in implicit solvent and I want to compute the
> > average force acting on the molecule at each frame. I tried to run the
> > following
> >
> > g_traj -f traj.trr -s traj.tpr -cf -af force.xvg
> >
> > but I get the following error:
> >
> > No frames found for average force, will not write force.pdb.
> >
> > The .trr and .tpr files are provided as output of the md simulation. What
> > am I doing wrong? Thanks.
> >
> > Simone
> > --
> >
> >
> --
> > Simone Orioli
> > PhD Student in Statistical Mechanics of Biomolecules
> >
> > Dipartimento di Fisica
> > Universita' degli Studi di Trento
> > Via Sommarive 14, Povo (Trento)
> > 38123, Italia
> >
> > Phone: +39 333 8116141
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[gmx-users] Possible to extract gro file from a tpr?

[ABEL Stephane]

Hi 

A quick question here, before to read this response I thought (but never 
tested) that it was possible to extract a pdb from a tpr since we use one to 
generate a tpr with grompp. So how is store the atomic coordinates of a system 
in a tpr file ?

Thanks  

--

Message: 1
Date: Tue, 3 Apr 2018 10:54:09 +0200
From: Viveca Lindahl 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Possible to extract gro file from a tpr?
Message-ID:

Re: [gmx-users] error in index file

[Joe Jordan]

Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.

On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal 
wrote:

> I'm using v4.6.2
>
> $make_ndx -f npt.gro
>
> > r 306 (residue num of ligand)
> > name 24 Ligand
>
> This should do the work right ?
>
> On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:
>
> > I got a group with the right number of atoms when I tried it. What
> version
> > of gromacs are you using and what selection string are you using?
> >
> > On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
> > wrote:
> >
> > > Location of the files:
> > > https://drive.google.com/drive/u/0/folders/0B6O-
> > > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
> > >
> > > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 
> > wrote:
> > >
> > > > Can you post the gro file and the resulting index file?
> > > >
> > > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
> > abhisek.m...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I'm just having some issue creating index file for umbrella
> sampling.
> > > > >
> > > > > I have a ligand:
> > > > > Group20 (NAP) has73 elements
> > > > >
> > > > > Now when I run following command:
> > > > > gmx make_ndx -f npt.gro
> > > > >
> > > > > and try to add NAP for index.ndx, only 6 elements were being added.
> > > > >
> > > > > I don't understand the problem here.
> > > > >
> > > > > NAP is clearly showing is of 73 elements, but how come it is
> showing
> > > me 6
> > > > > elements when added to index file ?
> > > > >
> > > > > Please help me out here.
> > > > >
> > > > > Thanks.
> > > > >
> > > > > --
> > > > > Abhisek Mondal
> > > > >
> > > > > *Senior Research Fellow*
> > > > >
> > > > > *Structural Biology and Bioinformatics Division*
> > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > >
> > > > > *Kolkata 700032*
> > > > >
> > > > > *INDIA*
> > > > > --
> > > > > 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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> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Joe Jordan
> > > > --
> > > > Gromacs Users mailing list
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> > > >
> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
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> > >
> >
> >
> >
> > --
> > Joe Jordan
> > --
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> >
>
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] error in index file

[abhisek Mondal]

I'm using v4.6.2

$make_ndx -f npt.gro

> r 306 (residue num of ligand)
> name 24 Ligand

This should do the work right ?

On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:

> I got a group with the right number of atoms when I tried it. What version
> of gromacs are you using and what selection string are you using?
>
> On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
> wrote:
>
> > Location of the files:
> > https://drive.google.com/drive/u/0/folders/0B6O-
> > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
> >
> > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 
> wrote:
> >
> > > Can you post the gro file and the resulting index file?
> > >
> > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
> abhisek.m...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I'm just having some issue creating index file for umbrella sampling.
> > > >
> > > > I have a ligand:
> > > > Group20 (NAP) has73 elements
> > > >
> > > > Now when I run following command:
> > > > gmx make_ndx -f npt.gro
> > > >
> > > > and try to add NAP for index.ndx, only 6 elements were being added.
> > > >
> > > > I don't understand the problem here.
> > > >
> > > > NAP is clearly showing is of 73 elements, but how come it is showing
> > me 6
> > > > elements when added to index file ?
> > > >
> > > > Please help me out here.
> > > >
> > > > Thanks.
> > > >
> > > > --
> > > > Abhisek Mondal
> > > >
> > > > *Senior Research Fellow*
> > > >
> > > > *Structural Biology and Bioinformatics Division*
> > > > *CSIR-Indian Institute of Chemical Biology*
> > > >
> > > > *Kolkata 700032*
> > > >
> > > > *INDIA*
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> or
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> > > >
> > >
> > >
> > >
> > > --
> > > Joe Jordan
> > > --
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> > >
> >
> >
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
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>
>
>
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] error in index file

[Joe Jordan]

I got a group with the right number of atoms when I tried it. What version
of gromacs are you using and what selection string are you using?

On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
wrote:

> Location of the files:
> https://drive.google.com/drive/u/0/folders/0B6O-
> L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
>
> On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan  wrote:
>
> > Can you post the gro file and the resulting index file?
> >
> > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > > I'm just having some issue creating index file for umbrella sampling.
> > >
> > > I have a ligand:
> > > Group20 (NAP) has73 elements
> > >
> > > Now when I run following command:
> > > gmx make_ndx -f npt.gro
> > >
> > > and try to add NAP for index.ndx, only 6 elements were being added.
> > >
> > > I don't understand the problem here.
> > >
> > > NAP is clearly showing is of 73 elements, but how come it is showing
> me 6
> > > elements when added to index file ?
> > >
> > > Please help me out here.
> > >
> > > Thanks.
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Joe Jordan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
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>
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-- 
Joe Jordan
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Re: [gmx-users] error in index file

[abhisek Mondal]

Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan  wrote:

> Can you post the gro file and the resulting index file?
>
> On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
> wrote:
>
> > Hi,
> >
> > I'm just having some issue creating index file for umbrella sampling.
> >
> > I have a ligand:
> > Group20 (NAP) has73 elements
> >
> > Now when I run following command:
> > gmx make_ndx -f npt.gro
> >
> > and try to add NAP for index.ndx, only 6 elements were being added.
> >
> > I don't understand the problem here.
> >
> > NAP is clearly showing is of 73 elements, but how come it is showing me 6
> > elements when added to index file ?
> >
> > Please help me out here.
> >
> > Thanks.
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Joe Jordan
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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Re: [gmx-users] error in index file

[Joe Jordan]

Can you post the gro file and the resulting index file?

On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
wrote:

> Hi,
>
> I'm just having some issue creating index file for umbrella sampling.
>
> I have a ligand:
> Group20 (NAP) has73 elements
>
> Now when I run following command:
> gmx make_ndx -f npt.gro
>
> and try to add NAP for index.ndx, only 6 elements were being added.
>
> I don't understand the problem here.
>
> NAP is clearly showing is of 73 elements, but how come it is showing me 6
> elements when added to index file ?
>
> Please help me out here.
>
> Thanks.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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.
>



-- 
Joe Jordan
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[gmx-users] error in index file

[abhisek Mondal]

Hi,

I'm just having some issue creating index file for umbrella sampling.

I have a ligand:
Group20 (NAP) has73 elements

Now when I run following command:
gmx make_ndx -f npt.gro

and try to add NAP for index.ndx, only 6 elements were being added.

I don't understand the problem here.

NAP is clearly showing is of 73 elements, but how come it is showing me 6
elements when added to index file ?

Please help me out here.

Thanks.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
Gromacs Users mailing list

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[gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

Hello,
I want to do the Spatial Distribution Function,
I tried to follow the manual gmx spatial.
I am following the five-step protocol which is given in gmx spatial manual..
1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
the Ow's of water molecules, Is this index good or should i have all the
molecules..??)
2) in the second step-  "gmx trjconv -s a.tpr
 -f a.tng
 -o b.tng
 -boxcenter tric -ur compact
-pbc none" here we need to give the input file ie., -f a.tng from where
does this .tng file i need to give the input..?? How do i create a .tng
file.. what information does this tng file contain...??

Any suggestions...

Thank you.
-- 
With Best Regards,

DILIP.H.N
Ph.D Student
‌
 Sent with Mailtrack

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Re: [gmx-users] Possible to extract gro file from a tpr?

[Viveca Lindahl]

Wish I could +1 the best response here :) Thanks.

--
Viveca


On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham 
wrote:

> Just say No! :-)
>
> On Fri, Mar 30, 2018, 19:58 Alex  wrote:
>
> > Or, and that is a very peculiar option, genion with -conc 0. :)
> >
> > Alex
> >
> >
> > On 3/30/2018 4:28 AM, Justin Lemkul wrote:
> > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl <
> vivecalind...@gmail.com>
> > > wrote:
> > >
> > >> Hi users,
> > >>
> > >> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx
> > mdrun
> > >> -nsteps 0' does not give a confout.gro :)
> > >>
> > > Just use editconf.
> > >
> > > -Justin
> > >
> > >
> > >> --
> > >> Viveca
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >> posting!
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> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> >
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