Re: [gmx-users] Batch mode error in GROMACS version 2019.2

[Rajib Biswas]

I did some more experimentation about this and found that this error is
coming only with the mpi enabled version.

Rajib

On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas  wrote:

> Hi Mark,
>
> Thanks!
>
> Interactively I could do it without any error. However, this error only
> arises whenever I have tried to use batch mode.
>
> With regards,
> *Rajib*
>
>
> On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham 
> wrote:
>
>> What happens when you do it interactively?
>>
>> Mark
>>
>> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas  wrote:
>>
>> > Dear All,
>> >
>> > I am trying to use the post-processing tools in batch mode. I am using
>> the
>> > following commands
>> >
>> > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
>> >
>> > Getting the following error:
>> >
>> > Program: gmx energy, version 2019.2
>> > Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
>> >
>> > Fatal error:
>> > No energy terms selected
>> >
>> >
>> > I have even tried all the options mentioned
>> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>> > however, could not get it worked for version 2019.2.
>> >
>> > Any help will be appreciated.
>> >
>> > With regards,
>> > *Rajib*
>> > --
>> > 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

* 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.

Re: [gmx-users] gromacs binaries for windows (Cygwin 64)

[yujie Liu]

It is great!

But, I think more effective is to enable CUDA (GPU) support.
https://www.dropbox.com/s/jtk5p7bz0ppgcbf/windows_gromacs2019.3%2Bfftw%2BintelC%2B%2B%2Bcuda10.rar?dl=0
here is a CUDA version of GROMACS 2019.3 by using VS 2017 and Intel C++,
which is support AVX2_256 and more effective because it can use your GPU.
More compile informations can been found my own wesit
https://liuyujie714.com/15.html



YuJie Liu
-- 
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.

[gmx-users] PMF wrong when calculating dihedral angle rotate

[yujie Liu]

Dear gmx users,
  I want to repeat a amber tutorial
*http://ambermd.org/tutorials/advanced/tutorial17/index.htm
* by using
gromacs, which is about PMF calculation of Alanine Dipeptide Phi/Psi
Rotation.
 Everything is ok about the process of simulation, firstly equilibrium and
generate a series of configuration, then do long simulation respectively.
  However, When using "gmx whan -it tpr.dat -if/x pullf/x.dat -cycl"
command  to generate PMF curve, I found histo.xvg figure is very good
but profile.xvg figure is wrong. Then I check the data of profile.xvg file,
found the second column data is "-nan". I also assign -min and -max, but
still wrong.
  Finally, I found same question on the internet, the URL is
*https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-August/108093.html
*
and *https://redmine.gromacs.org/issues/2609
* . At the same time, I repeat
this a sample PMF
(*https://redmine.gromacs.org/attachments/2405/gwham_error_sample.tar.gz
*)
about angle by "gmx wham", I also found "profile.xvg" is wrong.
  I use GROMACS 2019.3. I hope some expert can give me some good advice.
Whether the gromacs software can not generate correct PMF of angle?
  Thank you,
  YUjie Liu
-- 
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.

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

[Rajib Biswas]

Hi Mark,

Thanks!

Interactively I could do it without any error. However, this error only
arises whenever I have tried to use batch mode.

With regards,
*Rajib*


On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham 
wrote:

> What happens when you do it interactively?
>
> Mark
>
> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas  wrote:
>
> > Dear All,
> >
> > I am trying to use the post-processing tools in batch mode. I am using
> the
> > following commands
> >
> > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
> >
> > Getting the following error:
> >
> > Program: gmx energy, version 2019.2
> > Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
> >
> > Fatal error:
> > No energy terms selected
> >
> >
> > I have even tried all the options mentioned
> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> > however, could not get it worked for version 2019.2.
> >
> > Any help will be appreciated.
> >
> > With regards,
> > *Rajib*
> > --
> > 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

* 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.

Re: [gmx-users] Fat-bottom restrain

[Alex]

Hi Mark,

I am using Gromacs v.2018.x and as I tested it is not the matter of using
GPU or CPU.
The issue was from my side where by mistake I had put the wall (in all
posre.x,y,z.itp) exactly on the outer box borders so that my inner box and
outer box were fully identical,
so the molecules had no limitation and wherever of the simulation box they
could go, that is why the gmx energy shows the "Flat-bottom posres" portion
but it was absolutely zero.

However, my question now is; do I have flat-bottom restrains in these
simulation or not? e.g. If I want to report these simulations somewhere
should I mention that I have used (I haven't used) flat-bottom restrains in
these simulation?

Thank you
Alex

On Wed, Sep 11, 2019 at 8:01 PM Mark Abraham 
wrote:

> Hi,
>
> It's certainly conceivable that such restraints are ineffective in some run
> modes. However, "on the GPU" describes a range of scenarios. If you're
> running with 2019.x, does adding -bonded cpu to the mdrun command line
> restore the functionality?
>
> Otherwise, please try the "working CPU" run on a GPU resource and vice
> versa to see what we learn.
>
> Mark
>
> On Wed, 11 Sep 2019 at 23:21, Alex  wrote:
>
> > Thanks Billy,
> >
> > > If the flat bottom restraint energy is zero, then that means that the
> > > restraints aren't being applied, or your predefined distance is not
> being
> > > exceeded.  I doubt you would get binary zero values if it was the
> second
> > > option, so something is probably wrong with your syntax or your
> inclusion
> > > of the restraints
> >
> > As far as I have inspected everything is fine with the syntax and
> > application of the restraints. Using similar way works fine in another
> > system. The only difference is that one (not working one) runs on GPU and
> > the other one (the working one) runs on CPU, and I am not sure if that
> > plays any role and if the flat-bottom restrain doesn't work on GPU!
> >
> > >
> > > Cheers,
> > > Billy
> > >
> > > On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, <
> > > billy.williams-noo...@monash.edu> wrote:
> > >
> > > You may want to consider using smart-bottom restraints instead?
> > I haven't hear the smart-bottom one, would you please explain more? or
> > address me to a reference?
> > >
> > > Jokes aside, why does it matter if your molecules move into the next
> > > periodic image?
> > Just to avoid percolation across the period box.
> > >
> > > Cheers,
> > > Billy
> > Thank you,
> > Alex
> >
> > On Wed, Sep 11, 2019 at 3:02 AM Alex  wrote:
> >
> > > Hi,
> > >
> > > Any comment, please?
> > >
> > > Thank you.
> > > Alex
> > >
> > > On Mon, Sep 9, 2019 at 10:22 PM Alex 
> wrote:
> > >
> > >> Hi Mark,
> > >>
> > >> Thank you for your response.
> > >> Here are the part of options that gmx energy gives me out:
> > >>
> > >>   9  Coulomb-(SR)10  Coul.-recip.
> > >>  11  Flat-bottom-posres  12  Potential
> > >>  13  Kinetic-En. 14  Total-Energy15  Conserved-En
> > >>
> > >>
> > >> Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >>
> > >>
> >
> ---
> > >> Coulomb (SR) -8.4629e+061505041.75   -840.379
> > >> (kJ/mol)
> > >> Coul. recip.12689.7 12109.811   -83.8453
> > >> (kJ/mol)
> > >> Flat-bottom posres0  0  0  0
> > >> (kJ/mol)
> > >> Potential-7.29781e+065403208.53   -3702.71
> > >> (kJ/mol)
> > >> Kinetic En.  1.20527e+068.21912.61-12.144
> > >> (kJ/mol)
> > >> Total Energy -6.09255e+06540 3942.5   -3714.84
> > >> (kJ/mol)
> > >> Conserved En.-2.97263e+06 89 1.81911e+06
> 6.30101e+06
> > >> (kJ/mol)
> > >>
> > >> As can be seen above the Flat-bottom posres energy is just zero during
> > >> the simulation; and even stiffening the force constant from 4184
> > KJ/(mol.
> > >> nm^2) to 4184000  KJ/(mol. nm^2) doesn't change anythings and the
> > >> Flat-bottom posres energy would remain absolutely zero!
> > >>
> > >> I rechecked everything and I don't see any problem with the way I have
> > >> set the flat-bottom restrain.
> > >> Any comment would be highly appreciated.
> > >>
> > >> Thank you,
> > >> Alex
> > >>
> > >>
> > >>
> > >> On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham <
> mark.j.abra...@gmail.com>
> > >> wrote:
> > >>
> > >>> Hi,
> > >>>
> > >>> The total potential energy violating the restraints is reported, so
> you
> > >>> should see that there is an appropriate contribution there, and
> > probably
> > >>> plan to stiffen the force constant.
> > >>>
> > >>> Mark
> > >>>
> > >>> On Fri., 6 Sep. 2019, 17:23 Alex,  wrote:
> > >>>
> > >>> > Dear all,
> > >>> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to
> > have
> > >>> a
> > >>> > smaller cubic box as semi-preamble walls inside a bigger cubic box
> so
> > >>>

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

[Mark Abraham]

What happens when you do it interactively?

Mark

On Fri, 13 Sep 2019 at 14:21, Rajib Biswas  wrote:

> Dear All,
>
> I am trying to use the post-processing tools in batch mode. I am using the
> following commands
>
> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
>
> Getting the following error:
>
> Program: gmx energy, version 2019.2
> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
>
> Fatal error:
> No energy terms selected
>
>
> I have even tried all the options mentioned
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> however, could not get it worked for version 2019.2.
>
> Any help will be appreciated.
>
> With regards,
> *Rajib*
> --
> 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.

[gmx-users] Batch mode error in GROMACS version 2019.2

[Rajib Biswas]

Dear All,

I am trying to use the post-processing tools in batch mode. I am using the
following commands

echo 18 0 | gmx_mpi energy -f traj.edr -o temperature

Getting the following error:

Program: gmx energy, version 2019.2
Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)

Fatal error:
No energy terms selected


I have even tried all the options mentioned
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
however, could not get it worked for version 2019.2.

Any help will be appreciated.

With regards,
*Rajib*
-- 
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.

[gmx-users] Regarding obtaining potential energy using energy groups

[Nirali Desai]

Dear all
I have a system with 3 protein chains A B and C. I want to calculate the
potential energy between different chains.
I created energy groups by creating a new index file.
If I calculate potential energy between  C as one group and (AB) as another
group, will it contain the potential energy of interaction between A and B
too?

Your kind guidance in this matter is highly appreciated.


Thanking you,
Nirali Desai
-- 
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.

[gmx-users] error got while xpm2ps

[Kanwal Gill]

*Dear all,*
*I am simulating a system consisting of nanoparticles and biomolecules. I
have done the mdrun and doing the analysis part. i am doing dssp for
secondary structure, but got error while running xpm2ps as follows:*
gmx xpm2ps -f ss.xpm -o ss.eps
 -
-
-
-
-

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS:  gmx xpm2ps, version 2019.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:
 /home/asus/Documents/GOLD_Calcitonin/Analysis/antiparallel_protein
Command line:
  gmx xpm2ps -f ss.xpm -o ss.eps

There is 1 matrix in ss.xpm
Matrix 0 is 2224 x 63

---
Program: gmx xpm2ps, version 2019.1

Standard library logic error (bug):
(exception type: St11logic_error)
basic_string::_M_construct null not valid

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors.


*Please provide me the solution as soon as possible.*

*with regards, *
*Kanwal.*
-- 
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.

Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

[Tafelmeier, Stefanie]

Dear Mark,

many thanks for your answer.

Unfortunately I face another problem when installing Gromacs 2019.2 or 2019.3.

The regressiontests fail (no. 42 & 46).
This problem already occur when I installed Gromacs 2019.1. Then the issue was 
solved by using the newest versions of GCC and CUDA. 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/124028.html
 

If I want to do this now, I have the problem that the newest CUDA version does 
not support the newest GCC 
---
CMake Error at cmake/gmxManageNvccConfig.cmake:192 (message):
  NVCC/C++ compiler combination does not seem to be supported.  CUDA
  frequently does not support the latest versions of the host compiler, so
  you might want to try an earlier C++ compiler version and make sure your
  CUDA compiler and driver are as recent as possible.
---

Hence, I have to use the GCC 8.2, which then only allows me to use Gromacs 
2019.1 and so no annealing is possible. 
This is a bit tricky.

If you have any suggestions on how to use annealing anyway I would appreciate a 
lot.

Many thanks,
Steffi







-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Mark 
Abraham
Gesendet: Dienstag, 10. September 2019 17:56
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

Hi,

Thanks for the report - but it's probably fixed already (
http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html#fix-segmentation-fault-when-preparing-simulated-annealing-inputs)
so I suggest you get the latest 2019.x release?

Mark

On Tue, 10 Sep 2019 at 17:15, Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:

> Dear all,
>
> I try to use simulation annealing, but unfortunately the grompp - command
> leads to an error.
> It is not a known Gromacs error, but it doesn't finish the job and it
> says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means
> something like "Memory Access Error")
>
> The only output file produced is the mdout.mdp, which content seems
> correct.
>
> The screen text is given below as well as the grompp.mdp content and the
> details to the system used.
>
> There have been some issues as well to get Gromacs installed on the
> workstation. Not sure if this could be connected.
> Many thanks already for your help.
>
> Greetings,
> Steffi
>
>
>
> 
> Screen text:
>
> GROMACS:  gmx grompp, version 2019.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:
> /home/pcm-mess/Schreibtisch/StTa/Vergleich_FF/OPLS/fixed_layer/freeze_grp/temp_grps/annealing
> Command line:
>   gmx grompp -f grompp_OPLS_anneal.mdp -v
>
> checking input for internal consistency...
> Setting the LD random seed to -28800458
> processing topology...
> 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 'Other'
> turning all bonds into constraints...
>
> NOTE 1 [file unknown]:
>   You are using constraints on all bonds, whereas the forcefield has been
>   parametrized only with constraints involving hydrogen atoms. We suggest
>   using constraints = h-bonds instead, this will also improve performance.
>
> processing coordinates...
> double-checking input for internal consistency...
> Setting gen_seed to -1070611718
> Velocities were taken from a Maxwell distribution at 280 K
> Removing all charge groups because cutoff-scheme=Verlet
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> There are:  3600  Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Speicherzugriffsfehler (Speicherabzug geschrieben)
>
> 
>
>
> 
> Content grompp.mdp (as an example):
>
> include  = -I../top
> define   =
> cutoff-scheme= Verlet
> integrator   = md
> dt   = 0.001
> nsteps   = 80
> nstxout  = 2000
> nstvout  = 2000
> nstlog   = 2000
> nstenergy= 2000
> nstlist  = 10
> ns-type  = grid
> pbc  = xyz
> rlist= 1
> coulombtype  = PME
> rcoulomb = 1
> rvdw = 1
> tcoupl   = v-rescale
> tc-grps = other
> tau-t= 0.1
>