Re: [gmx-users] Gromacs error

[Dallas Warren]

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-covar.html
Has the following note (as does 'gmx help covar'):
"Note that the diagonalization of a matrix requires memory and time
that will increase at least as fast as than the square of the number
of atoms involved. It is easy to run out of memory, in which case this
tool will probably exit with a ‘Segmentation fault’. You should
consider carefully whether a reduced set of atoms will meet your needs
for lower costs."

Plus see http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory

So it appears that the system size is too large to be able to perform
the calculation with the computer memory that you have available.  See
last link for suggestions on how to solve.

Catch ya,

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

On Wed, 29 May 2019 at 22:11, Budheswar Dehury  wrote:
>
> Dear GROMACS Developers and users,
>
> While trying to clustering analysis based on certain distance matrices, 
> however, while trying to perform PCA, I executed the following command, it 
> shows the following error. Need your valuable suggestion and feedback to get 
> rid of such errors.
>
> Thanking you
> Budheswar
>
> gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc
>   :-) GROMACS - gmx covar, 2019.2 (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. 
> Berendsen
> Par Bjelkmar  Christian Blau   Viacheslav Bolnykh Kevin Boyd
>  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Alan Gray
>   Gerrit Groenhof Anca HamuraruVincent Hindriksen  M. Eric Irrgang
>   Aleksei Iupinov   Christoph Junghans Joe Jordan Dimitrios Karkoulis
> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>   Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund
> Pascal Merz Pieter MeulenhoffTeemu Murtola   Szilard Pall
> Sander Pronk  Roland Schulz  Michael ShirtsAlexey Shvetsov
>Alfons Sijbers Peter Tieleman  Jon Vincent  Teemu Virolainen
>  Christian WennbergMaarten Wolf
>and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2018, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> 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 covar, version 2019.2
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/bd422/Desktop/BD/1
> Command line:
>   gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc
>
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>  based on residue and atom names, since they could not be
>  definitively assigned from the information in your input
>  files. These guessed numbers might deviate from the mass
>  and radius of the atom type. Please check the output
>  files if necessary.
>
>
> Choose a group for the covariance analysis
> Group 0 ( System) has 66506 elements
> Group 1 (Protein) has 66506 elements
> Group 2 (  Protein-H) has 66506 elements
> Group 3 (C-alpha) has 66506 elements
> Group 4 (   Backbone) has 66506 elements
> Group 5 (  MainChain) has 66506 elements
> Group 6 (   MainChain+Cb) has 66506 elements
> Group 7 (MainChain+H) has 66506 elements
> Group 8 (  SideChain) has 0 elements
> Group 9 (SideChain-H) has 0 elements
> Select a group: 0
> Selected 0: 'System'
>
> ---
> Program: gmx covar, version 2019.2
> Source file: src/gromacs/utility/smalloc.cpp (line 125)
>
> Fatal error:
> Not enough memory. Failed to calloc 39807432324 elements of size 4 for mat
> (called from file
> /home/bd422/Downloads/gromacs-2019.2/src/gromacs/gmxana/gmx_covar.cpp, line
> 260)
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> --
> 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 

[gmx-users] Gromacs error

[Budheswar Dehury]

Dear GROMACS Developers and users,

While trying to clustering analysis based on certain distance matrices, 
however, while trying to perform PCA, I executed the following command, it 
shows the following error. Need your valuable suggestion and feedback to get 
rid of such errors.

Thanking you
Budheswar

gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc
  :-) GROMACS - gmx covar, 2019.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. Berendsen
Par Bjelkmar  Christian Blau   Viacheslav Bolnykh Kevin Boyd
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Alan Gray
  Gerrit Groenhof Anca HamuraruVincent Hindriksen  M. Eric Irrgang
  Aleksei Iupinov   Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund
Pascal Merz Pieter MeulenhoffTeemu Murtola   Szilard Pall
Sander Pronk  Roland Schulz  Michael ShirtsAlexey Shvetsov
   Alfons Sijbers Peter Tieleman  Jon Vincent  Teemu Virolainen
 Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

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 covar, version 2019.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/bd422/Desktop/BD/1
Command line:
  gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc


WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.


Choose a group for the covariance analysis
Group 0 ( System) has 66506 elements
Group 1 (Protein) has 66506 elements
Group 2 (  Protein-H) has 66506 elements
Group 3 (C-alpha) has 66506 elements
Group 4 (   Backbone) has 66506 elements
Group 5 (  MainChain) has 66506 elements
Group 6 (   MainChain+Cb) has 66506 elements
Group 7 (MainChain+H) has 66506 elements
Group 8 (  SideChain) has 0 elements
Group 9 (SideChain-H) has 0 elements
Select a group: 0
Selected 0: 'System'

---
Program: gmx covar, version 2019.2
Source file: src/gromacs/utility/smalloc.cpp (line 125)

Fatal error:
Not enough memory. Failed to calloc 39807432324 elements of size 4 for mat
(called from file
/home/bd422/Downloads/gromacs-2019.2/src/gromacs/gmxana/gmx_covar.cpp, line
260)

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

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[gmx-users] Gromacs error while running energy minimization step

[Muneeswaran S]

I got the following error while running the gromacs

























*NOTE: disabling dynamic load balancing as it is only supported with
dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP
threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected
for this run.Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this
node:
PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1---Program:
gmx mdrun, version 2018.6Source file: src/gromacs/utility/filestream.cpp
(line 115)Function:gmx::internal::FileStreamImpl::FileStreamImpl(const
char*, const char*)MPI rank:12 (out of 16)System I/O error:Failed to
compile NBNXN kernels for GPU #Quadro P620  Could not open file
'/usr/share/gromacs/opencl/nbnxn_ocl_kernels.cl
'Reason: No such file or directory
(call to fopen() returned error code 2)For more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
*
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Re: [gmx-users] gromacs error in vacuum preparation simulation

[Mario Andres Rodriguez Pineda]

Thanks, for your help.

Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul 
escreveu:

>
>
> On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:
> > If i don't use -maxwarn option they send me the same error.
>
> Omitting -maxwarn won't fix problems, but it is a very bad habit to
> casually use -maxwarn as it overrides critical problems with your input.
>
> > I see also this:
> > WARNING 1 [file topol.top, line 23986]:
> >You are using Ewald electrostatics in a system with net charge. This
> can
> >lead to severe artifacts, such as ions moving into regions with low
> >dielectric, due to the uniform background charge. We suggest to
> >neutralize your system with counter ions, possibly in combination
> with a
> >physiological salt concentration.
> > Cheking the archive toppol.top this line is empty
> >
> > I'm try to minimize the energy of my protein in vacum, whithout ions or
> > solvent
>
> As the message says, you shouldn't be using PME for this system. In
> vacuum, you should be using plain cutoff electrostatics with infinite
> cutoffs (rlist=rcoulomb=rvdw=0).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>


-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
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Re: [gmx-users] gromacs error in vacuum preparation simulation

[Justin Lemkul]

On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:

If i don't use -maxwarn option they send me the same error.


Omitting -maxwarn won't fix problems, but it is a very bad habit to 
casually use -maxwarn as it overrides critical problems with your input.



I see also this:
WARNING 1 [file topol.top, line 23986]:
   You are using Ewald electrostatics in a system with net charge. This can
   lead to severe artifacts, such as ions moving into regions with low
   dielectric, due to the uniform background charge. We suggest to
   neutralize your system with counter ions, possibly in combination with a
   physiological salt concentration.
Cheking the archive toppol.top this line is empty

I'm try to minimize the energy of my protein in vacum, whithout ions or
solvent


As the message says, you shouldn't be using PME for this system. In 
vacuum, you should be using plain cutoff electrostatics with infinite 
cutoffs (rlist=rcoulomb=rvdw=0).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] gromacs error in vacuum preparation simulation

[Mario Andres Rodriguez Pineda]

If i don't use -maxwarn option they send me the same error.
I see also this:
WARNING 1 [file topol.top, line 23986]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.
Cheking the archive toppol.top this line is empty

I'm try to minimize the energy of my protein in vacum, whithout ions or
solvent

Em seg, 11 de mar de 2019 às 17:12, Justin Lemkul 
escreveu:

>
>
> On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:
> > Hi everybody
> > I want to do one dynamic simulation of one protein
> > i'm try to minimize the protein in vacum before the simulation runing but
> > gromacs send me this error:
> > ---
> > Program: gmx grompp, version 2018.6
> > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)
> >
> > Fatal error:
> > There was 1 error in input file(s)
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> >
> --
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --
> > this is the command that i use for minimization in vacum.
> > gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o
> > cbd212_vac.tpr -maxwarn 1
>
> Run grompp interactively if you want to see the actual error. It may
> also be printed to a log file from your queuing system. Also, never use
> -maxwarn.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>


-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
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Re: [gmx-users] gromacs error in vacuum preparation simulation

[Justin Lemkul]

On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:

Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program: gmx grompp, version 2018.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
this is the command that i use for minimization in vacum.
gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o
cbd212_vac.tpr -maxwarn 1


Run grompp interactively if you want to see the actual error. It may 
also be printed to a log file from your queuing system. Also, never use 
-maxwarn.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] gromacs error in vacuum preparation simulation

[Mario Andres Rodriguez Pineda]

Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program: gmx grompp, version 2018.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
this is the command that i use for minimization in vacum.
gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o
cbd212_vac.tpr -maxwarn 1


I can't find the solution for this problem.

Thanks for your help
-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
-- 
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] Gromacs error

[Vytautas Rakeviius]

You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF
 

On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta 
 wrote:  
 
 Hi,
I have the following problems

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON

CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):

  The GROMACS build will download FFTW 3.3.3 as requested, but it will not

  know the file it receives is correct.  If you now use



  make



  GROMACS will build and link to FFTW anyway, but there is a possible
security risk if you execute a GROMACS tool that calls this library.
Instead, you can use



  make fftwBuild



  to do just the download and build of FFTW, and then run



  md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz



  to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2.  If so, everything

  is OK and you should use



  make



  to proceed with the rest of the GROMACS build. Alternatively, you could
stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation
instructions to build FFTW yourself.





-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2

-- Configuring done

-- Generating done

-- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make

[  1%] Built target fftwBuild

[  1%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o

/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
void*, size_t)’:

/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope

  return (char *) memcpy (__dest, __src, __n) + __n;

                                          ^

CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:264 (message):

  Error generating file


/home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o





src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383:
recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o'
failed

make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1

CMakeFiles/Makefile2:1609: recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed

make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2

Makefile:147: recipe for target 'all' failed

make: *** [all] Error 2
-- 
-
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933

ORCID ID: -0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284J=en

-- 





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[gmx-users] Gromacs error

[Kunal Dutta]

Hi,
I have the following problems

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON

CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):

  The GROMACS build will download FFTW 3.3.3 as requested, but it will not

  know the file it receives is correct.  If you now use



  make



   GROMACS will build and link to FFTW anyway, but there is a possible
security risk if you execute a GROMACS tool that calls this library.
Instead, you can use



  make fftwBuild



   to do just the download and build of FFTW, and then run



  md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz



  to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2.  If so, everything

  is OK and you should use



  make



   to proceed with the rest of the GROMACS build. Alternatively, you could
stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation
instructions to build FFTW yourself.





-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2

-- Configuring done

-- Generating done

-- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make

[  1%] Built target fftwBuild

[  1%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o

/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
void*, size_t)’:

/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope

   return (char *) memcpy (__dest, __src, __n) + __n;

  ^

CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:264 (message):

  Error generating file


/home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o





src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383:
recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o'
failed

make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1

CMakeFiles/Makefile2:1609: recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed

make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2

Makefile:147: recipe for target 'all' failed

make: *** [all] Error 2
-- 
-
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933

ORCID ID: -0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284J=en

-- 





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*DISCLAIMER*
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Re: [gmx-users] gromacs error

[Justin Lemkul]

On 10/16/17 12:17 PM, Rahma Dahmani wrote:

Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.


Either correct the atom names to what the force field expects, or 
simplify life and use -ignh to have pdb2gmx rebuild the H atoms.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] gromacs error

[Rahma Dahmani]

Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.

Thank you for your help
-- 






*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*
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Re: [gmx-users] gromacs error

[Mark Abraham]

Hi,

It's hard to say, but you should look at the log file and terminal output,
and install the latest in the series of bug fixes... 5.0.7 rather than
choose a version known to have dozens more bugs...

Mark

On Tue, Sep 12, 2017 at 3:55 PM Vidya R  wrote:

> Hi,
>
> I fixed that error.
>
> However,I now encounter a new one...
>
> GROMACS:gmx grompp, VERSION 5.0.2
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
> Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
> Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
> Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
> Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
> Peter Tieleman Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> 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 grompp, VERSION 5.0.2
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx grompp -f mdp/min.mdp -o min -pp min -po min
>
> Setting the LD random seed to 1842076191
> Generated 349030 of the 349030 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 349030 of the 349030 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'LIG'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Removing all charge groups because cutoff-scheme=Verlet
> Number of degrees of freedom in T-Coupling group rest is 11837.00
> Estimate for the relative computational load of the PME mesh part: 0.17
>
> gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)
>
> GROMACS:gmx mdrun, VERSION 5.0.2
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
> Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
> Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
> Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
> Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
> Peter Tieleman Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> 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 mdrun, VERSION 5.0.2
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min
>
> Reading file min.tpr, VERSION 5.0.2 (single precision)
> Using 1 MPI thread
> Using 8 OpenMP threads
> mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
> exited on signal 11 (Segmentation fault).
>
>
> What is segmentation fault?
>
> What am I supposed to do?
>
> Please tell me.
>
> Thanks,
> Vidya.R
>
>
> On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Yeah I've never seen that, so I assume it's something weird related to
> how
> > GROMACS was originally compiled vs how the system has been updated since.
> > Since a rebuild is the way to investigate that, definitely update to at
> > least the latest 5.0.x while you do it.
> >
> > Mark
> >
> > On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett 
> > wrote:
> >
> > > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R 
> > wrote:
> > >
> > > > Hi,
> > > >
> > > >
> > > > When I give these two commands
> > > >
> > > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > > gmx mdrun -deffnm min
> > > >
> > > > I get this error.
> > > >
> > > > What to do?
> > > >
> > > >
> > > >
> > > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > > tMPI error: 

Re: [gmx-users] gromacs error

[Vidya R]

Hi,

I fixed that error.

However,I now encounter a new one...

GROMACS:gmx grompp, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

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 grompp, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx grompp -f mdp/min.mdp -o min -pp min -po min

Setting the LD random seed to 1842076191
Generated 349030 of the 349030 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 349030 of the 349030 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'LIG'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 11837.00
Estimate for the relative computational load of the PME mesh part: 0.17

gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)

GROMACS:gmx mdrun, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

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 mdrun, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min

Reading file min.tpr, VERSION 5.0.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
exited on signal 11 (Segmentation fault).


What is segmentation fault?

What am I supposed to do?

Please tell me.

Thanks,
Vidya.R


On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham 
wrote:

> Hi,
>
> Yeah I've never seen that, so I assume it's something weird related to how
> GROMACS was originally compiled vs how the system has been updated since.
> Since a rebuild is the way to investigate that, definitely update to at
> least the latest 5.0.x while you do it.
>
> Mark
>
> On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett 
> wrote:
>
> > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R 
> wrote:
> >
> > > Hi,
> > >
> > >
> > > When I give these two commands
> > >
> > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > gmx mdrun -deffnm min
> > >
> > > I get this error.
> > >
> > > What to do?
> > >
> > >
> > >
> > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > tMPI error: tMPI Initialization error (in valid comm)
> > >
> > > Thanks,
> > > Vidya.R
> > >
> >
> > I can't speak to that exact error, but there have been several bug fix
> > releases to the 5.0.x series since 5.0.2, so an upgrade may be in order.
> I
> > would even suggest upgrading to the latest release (2016.x series).
> >
> >
> > --
> > James "Wes" Barnett
> > Postdoctoral Research Scientist
> > Department of Chemical Engineering
> > Kumar Research Group 
> > Columbia University
> > 

Re: [gmx-users] gromacs error

[Mark Abraham]

Hi,

Yeah I've never seen that, so I assume it's something weird related to how
GROMACS was originally compiled vs how the system has been updated since.
Since a rebuild is the way to investigate that, definitely update to at
least the latest 5.0.x while you do it.

Mark

On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett  wrote:

> On Mon, Sep 11, 2017 at 8:44 AM, Vidya R  wrote:
>
> > Hi,
> >
> >
> > When I give these two commands
> >
> > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > gmx mdrun -deffnm min
> >
> > I get this error.
> >
> > What to do?
> >
> >
> >
> > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > tMPI error: tMPI Initialization error (in valid comm)
> >
> > Thanks,
> > Vidya.R
> >
>
> I can't speak to that exact error, but there have been several bug fix
> releases to the 5.0.x series since 5.0.2, so an upgrade may be in order. I
> would even suggest upgrading to the latest release (2016.x series).
>
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group 
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
> --
> 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] gromacs error

[Wes Barnett]

On Mon, Sep 11, 2017 at 8:44 AM, Vidya R  wrote:

> Hi,
>
>
> When I give these two commands
>
> gmx grompp -f mdp/min.mdp -o min -pp min -po min
> gmx mdrun -deffnm min
>
> I get this error.
>
> What to do?
>
>
>
> Reading file min.tpr, VERSION 5.0.2 (single precision)
> tMPI error: tMPI Initialization error (in valid comm)
>
> Thanks,
> Vidya.R
>

I can't speak to that exact error, but there have been several bug fix
releases to the 5.0.x series since 5.0.2, so an upgrade may be in order. I
would even suggest upgrading to the latest release (2016.x series).


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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[gmx-users] gromacs error

[Vidya R]

Hi,


When I give these two commands

gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min

I get this error.

What to do?



Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)

Thanks,
Vidya.R
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Re: [gmx-users] Gromacs error: equilibration phase

[Deep kumar]

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".

c) submitted the entry and after completion, downloaded the file as below:

>From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html)
says, I have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?

Thanks,
Deep

On Tue, Sep 5, 2017 at 4:04 PM, Deep kumar 
wrote:

> Dear All,
>
> I have a query regarding Gromacs run. The error when running the
> "equilibration phase". I am following the tutorial from here:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/complex/06_equil.html
> 
>
> I am trying to prepare a system for MD run of 20ns for the pdb "4NYM". For
> the same I prepared two pdb files; 4NYM_clean.pdb (without ligands,
> GNP[ligand2.pdb] & RND[ligand3.pdb]) & 4NYM.pdb (with ligands). I produced
> the .itp and .gro files of the ligands separately using "prodrg"
> (attached). "posre_GNP.itp" & "posre_RND.itp" files were produced using
> gromacs tutorial by "gmx genrestr". All steps went well without error until
> the "nvt.mdp" equilibration run. I have attached the pdb files and the .mdp
> files I used. I have also attached a produced pdb (step0c.pdb) file just
> before the "nvt" crash/error.
>
> minim.mdp: is the file used to get "ions.tpr"
> em_real.mdp: for energy minimization
> nvt.mdp: for first equilibration phase
>
> The error I get is:
>
> [root@g ras-sos]# gmx mdrun -deffnm nvt
>
> :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
>
>
>
> GROMACS is written by:
>
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
>
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
>
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
>
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
>
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
>
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
>
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
>
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
>
> and the project leaders:
>
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
>
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>
> Copyright (c) 2001-2015, The GROMACS development team at
>
> Uppsala University, Stockholm University and
>
> the Royal Institute of Technology, Sweden.
>
> check out http://www.gromacs.org
>  for
> more information.
>
>
>
> 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 mdrun, VERSION 5.1.4
>
> Executable: /usr/local/gromacs/bin/gmx
>
> Data prefix: /usr/local/gromacs
>
> Command line:
>
> gmx mdrun -deffnm nvt
>
>
>
>
>
> Back Off! I just backed up nvt.log to ./#nvt.log.6#
>
>
>
> Running on 1 node with total 4 cores, 4 logical cores
>
> Hardware detected:
>
> CPU info:
>
> Vendor: GenuineIntel
>
> Brand: Intel(R) Xeon(R) CPU E3-1220 v3 @ 3.10GHz
>
> SIMD instructions most likely to fit this hardware: AVX2_256
>
> SIMD instructions selected at GROMACS compile time: AVX2_256
>
>
>
> Reading file nvt.tpr, VERSION 5.1.4 (single precision)
>
> Changing nstlist from 10 to 25, rlist from 1.4 to 1.433
>
>
>
> Using 1 MPI thread
>
> Using 4 OpenMP threads
>
>
>
>
>
> Back Off! I just backed up nvt.trr to ./#nvt.trr.6#
>
>
>
> Back Off! I just backed up 

Re: [gmx-users] gromacs error

[Justin Lemkul]

On 8/29/17 12:09 AM, Neha Gupta wrote:

Hi Vytautas,

Thank you for your response..

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

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

But the error tells me :

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

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

What is the next step?


It's hard to even follow what you've done.  If GROMACS couldn't find 
FFTW when installing, even that should have failed.  It appears you've 
compiled FFTW statically whereas GROMACS expected shared objects.  
Revisit how you compiled everything, and perhaps start over so you do 
things consistently.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] gromacs error

[Neha Gupta]

Hi Vytautas,

Thank you for your response..

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

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

But the error tells me :

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

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

What is the next step?

Thanks,
Neha

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

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

[Vytautas Rakeviius]

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

Hi gromacs users,

How to fix this error?

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

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

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



Thanks,
Neha
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[gmx-users] gromacs error

[Neha Gupta]

Hi gromacs users,

How to fix this error?

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

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

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



Thanks,
Neha
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Re: [gmx-users] gromacs error

[Justin Lemkul]

On 2/1/16 1:06 AM, Mehreen Jan wrote:

how to run gromacs for protein protein interaction having phosphorylated at SER 
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields


make changes in .rtp file

make changes in .dat file
forcefield 43A1 is used.

command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
error:
residue "TPO" not found in residue topology database



This means whatever either (1) you did not make the changes in the 
directory/file you thought or (2) you did not choose the right force field when 
prompted by pdb2gmx.  Without the full screen output from pdb2gmx, it's 
impossible to tell.


-Justin


make changes in residuestypes.dat
fallowing are the changes make in .rtp file

; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms


[ SEP ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH2 0.0 2
OGOA-0.36000 2
 P P 0.94000 2
   O1POP-0.86000 2
   O2POP-0.86000 2
   O3POP-0.86000 2
 C C   0.380 3
 O O  -0.380 3
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26
CBOGgb_17
OG Pgb_27
 P   O1Pgb_23
 P   O2Pgb_23
 P   O3Pgb_23
[ angles ]
;  aiajak   gromos type
-C N H ga_31
 H NCA ga_17
-C NCA ga_30
 NCA C ga_12
CA C+N ga_18
CA C O ga_29
 O C+N ga_32
 NCACB ga_12
 CCACB ga_12
CACBOG ga_12
CBOG P ga_25
OG P   O1P ga_13
OG P   O2P ga_13
OG P   O3P ga_13
   O1P P   O2P ga_28
   O1P P   O3P ga_28
   O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
 N-CCA H gi_1
 CCA+N O gi_1
CA N CCB gi_2
[ dihedrals ]
;  aiajakal   gromos type
   -CA-C NCA gd_4
-C NCA C gd_19
 NCA C+N gd_20
 NCACBOG gd_17
CACBOG P gd_14
CBOG P   O1P gd_11

[ TPO ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH1 0.0 2
   OG1OA-0.36000 2
 P P 0.94000 2
   O1POP-0.86000 2
   O2POP-0.86000 2
   O3POP-0.86000 2
   CG2   CH3 0.0 3
 C C   0.380 4
 O O  -0.380 4
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26
CB   OG1gb_17
CB   CG2gb_26
   OG1 Pgb_27
 P   O1Pgb_23
 P   O2Pgb_23
 P   O3Pgb_23
[ angles ]
;  aiajak   gromos type
-C N H ga_31
 H NCA ga_17
-C NCA ga_30
 NCA C ga_12
CA C+N ga_18
CA C O ga_29
 O C+N ga_32
 NCACB ga_12
 CCACB ga_12
CACB   OG1 ga_12
CACB   CG2 ga_14
   OG1CB   CG2 ga_14
CB   OG1 P ga_25
   OG1 P   O1P ga_13
   OG1 P   O2P ga_13
   OG1 P   O3P ga_13
   O1P P   O2P ga_28
   O1P P   O3P ga_28
   O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
 N-CCA H gi_1
 CCA+N O gi_1
CA N CCB gi_2
CB   OG1   CG2CA gi_2
[ dihedrals ]
;  aiajakal   gromos type
   -CA-C NCA gd_4
-C NCA C gd_19
 NCA C+N gd_20
 NCACB   OG1 gd_17
CACB   OG1 P gd_14
CB   OG1 P   O1P gd_11

[ PTR ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH2 0.0 1
CG C 0.0 1
   CD1 C-0.1 2
   HD1HC 0.1 2
   CD2 C-0.1 3
   HD2HC 0.1 3
   CE1 C-0.1 4
   HE1HC 0.1 4
   CE2 C-0.1 5
   HE2HC 0.1 5
CZ C 0.0 6
OHOA-0.36000 6
 P P 0.94000 6
   O1POP-0.86000 6
   O2POP-0.86000 6
   O3POP-0.86000 6
 C C   0.380 7
 O O  -0.380 7
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26

Re: [gmx-users] gromacs error

[Mehreen Jan]

how to run gromacs for protein protein interaction having phosphorylated at SER 
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields

>make changes in .rtp file
make changes in .dat file
forcefield 43A1 is used.

command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
error:
residue "TPO" not found in residue topology database

make changes in residuestypes.dat
fallowing are the changes make in .rtp file

; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms


[ SEP ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 2
   OGOA-0.36000 2
P P 0.94000 2
  O1POP-0.86000 2
  O2POP-0.86000 2
  O3POP-0.86000 2
C C   0.380 3
O O  -0.380 3
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CBOGgb_17   
   OG Pgb_27   
P   O1Pgb_23   
P   O2Pgb_23   
P   O3Pgb_23   
[ angles ]
;  aiajak   gromos type
   -C N H ga_31   
H NCA ga_17   
   -C NCA ga_30   
NCA C ga_12   
   CA C+N ga_18   
   CA C O ga_29   
O C+N ga_32   
NCACB ga_12   
CCACB ga_12   
   CACBOG ga_12   
   CBOG P ga_25
   OG P   O1P ga_13
   OG P   O2P ga_13
   OG P   O3P ga_13
  O1P P   O2P ga_28
  O1P P   O3P ga_28
  O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1   
CCA+N O gi_1   
   CA N CCB gi_2   
[ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_4   
   -C NCA C gd_19   
NCA C+N gd_20   
NCACBOG gd_17   
   CACBOG P gd_14   
   CBOG P   O1P gd_11

[ TPO ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH1 0.0 2
  OG1OA-0.36000 2
P P 0.94000 2
  O1POP-0.86000 2
  O2POP-0.86000 2
  O3POP-0.86000 2
  CG2   CH3 0.0 3
C C   0.380 4
O O  -0.380 4
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CB   OG1gb_17   
   CB   CG2gb_26   
  OG1 Pgb_27   
P   O1Pgb_23   
P   O2Pgb_23   
P   O3Pgb_23   
[ angles ]
;  aiajak   gromos type
   -C N H ga_31   
H NCA ga_17   
   -C NCA ga_30   
NCA C ga_12   
   CA C+N ga_18   
   CA C O ga_29   
O C+N ga_32   
NCACB ga_12   
CCACB ga_12   
   CACB   OG1 ga_12   
   CACB   CG2 ga_14   
  OG1CB   CG2 ga_14   
   CB   OG1 P ga_25
  OG1 P   O1P ga_13
  OG1 P   O2P ga_13
  OG1 P   O3P ga_13
  O1P P   O2P ga_28
  O1P P   O3P ga_28
  O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1   
CCA+N O gi_1   
   CA N CCB gi_2   
   CB   OG1   CG2CA gi_2   
[ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_4   
   -C NCA C gd_19   
NCA C+N gd_20   
NCACB   OG1 gd_17   
   CACB   OG1 P gd_14   
   CB   OG1 P   O1P gd_11

[ PTR ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 1
   CG C 0.0 1
  CD1 C-0.1 2
  HD1HC 0.1 2
  CD2 C-0.1 3
  HD2HC 0.1 3
  CE1 C-0.1 4
  HE1HC 0.1 4
  CE2 C-0.1 5
  HE2HC 0.1 5
   CZ C 0.0 6
   OHOA-0.36000 6
P P 0.94000 6
  O1POP-0.86000 6
  O2POP-0.86000 6
  O3POP-0.86000 6
C C   0.380 7
O O  -0.380 7
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CBCGgb_26   
   CG   CD1gb_15   
   CG   CD2gb_15   
  CD1   HD1gb_3   
  CD1   CE1gb_15   
  CD2   HD2gb_3   
  CD2   CE2gb_15   
  CE1   HE1gb_3   
  CE1CZgb_15   
  CE2   

[gmx-users] gromacs error

[Puneet]

Hello 

 

I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error ? 

 

Error

 

Program grompp, version 3.3.3

source code file: toppush.c, line: 1396

 

Fatal error:

No such moleculetype NA

 

Please reply as soon as possible its really urgent for me.

 

Regards

Puneet Kaur

 

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Re: [gmx-users] gromacs error

[Smith, Micholas D.]

Check your topology file (.top) and make sure you have ions.itp imported and 
that you are using the proper naming convention of sodium for your force-field.

Hope that helps.

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Puneet 
<puneet.k...@adibackoffice.net>
Sent: Wednesday, December 09, 2015 7:33 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs error

Hello



I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error ?



Error



Program grompp, version 3.3.3

source code file: toppush.c, line: 1396



Fatal error:

No such moleculetype NA



Please reply as soon as possible its really urgent for me.



Regards

Puneet Kaur



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Re: [gmx-users] Gromacs Error

[Tsjerk Wassenaar]

Hi Manoj,

The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.

Cheers,

Tsjerk
On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in
wrote:

 Dear All,
 i'm geting below error while subjecting my system (Protein-ligand) for
 equlibriation in nvt.mdp file

 mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro
 -p topol.top -n index.ndx -o nvt.tpr
  :-)  G  R  O  M  A  C  S  (-:

GRowing Old MAkes el Chrono Sweat

 :-)  VERSION 4.5.3  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University  The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

 :-)  grompp  (-:

 Option Filename  Type Description
 
   -fnvt.mdp  Inputgrompp input file with MD parameters
  -po  mdout.mdp  Output   grompp input file with MD parameters
   -c em.gro  InputStructure file: gro g96 pdb tpr etc.
   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
   -n  index.ndx  Input, Opt!  Index file
   -p  topol.top  InputTopology file
  -pp  processed.top  Output, Opt. Topology file
   -onvt.tpr  Output   Run input file: tpr tpb tpa
   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
   -e   ener.edr  Input, Opt.  Energy file

 Option   Type   Value   Description
 --
 -[no]h   bool   no  Print help info and quit
 -[no]version bool   no  Print version info and quit
 -niceint0   Set the nicelevel
 -[no]v   bool   no  Be loud and noisy
 -timereal   -1  Take frame at or first after this time.
 -[no]rmvsbds bool   yes Remove constant bonded interactions with
 virtual
 sites
 -maxwarn int0   Number of allowed warnings during input
 processing
 -[no]zerobool   no  Set parameters for bonded interactions without
 defaults to zero instead of generating an error
 -[no]renum   bool   yes Renumber atomtypes and minimize number of
 atomtypes

 Ignoring obsolete mdp entry 'title'

 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#

 ERROR 1 [file nvt.mdp]:
   With coulombtype = PME-Switch, rcoulomb must be = rlist

 Generated 279 of the 1225 non-bonded parameter combinations
 Excluding 3 bonded neighbours molecule type 'Protein'
 turning all bonds into constraints...
 Excluding 3 bonded neighbours molecule type 'UNT'
 turning all bonds into constraints...
 Excluding 2 bonded neighbours molecule type 'SOL'
 turning all bonds into constraints...
 Excluding 1 bonded neighbours molecule type 'CL'
 turning all bonds into constraints...
 Setting gen_seed to 3507
 Velocities were taken from a Maxwell distribution at 300 K

 ---
 Program grompp, VERSION 4.5.3
 Source code file: grompp.c, line: 1356

 Fatal error:
 There was 1 error in input file(s)
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 Yeah, a Wuzz, Or a Jerk (F. Black)
  With Best Regards.

 Mr.Manoj Damale,
 M.S. Pharma (Pharmacoinformatics) NIPER,
 Kolkata, West Bengal State,
 India.
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 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] Gromacs Error

[Tsjerk Wassenaar]

ERROR 1 [file nvt.mdp]:
  With coulombtype = PME-Switch, rcoulomb must be = rlist

On Tue, May 19, 2015 at 10:25 AM, manoj damale 
manojaurangabad...@yahoo.co.in wrote:

 what exactly i should modify

 With Best Regards.


 Mr.Manoj Damale,
 M.S. Pharma (Pharmacoinformatics) NIPER,
 Kolkata, West Bengal State,
 India.



   On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar tsje...@gmail.com
 wrote:


 Hi Manoj,
 The error is clear. Check the settings referred to in your .mdp file and
 modify them accordingly.
 Cheers,
 Tsjerk
 On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in
 wrote:

 Dear All,
 i'm geting below error while subjecting my system (Protein-ligand) for
 equlibriation in nvt.mdp file

 mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro
 -p topol.top -n index.ndx -o nvt.tpr
  :-)  G  R  O  M  A  C  S  (-:

GRowing Old MAkes el Chrono Sweat

 :-)  VERSION 4.5.3  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University  The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

 :-)  grompp  (-:

 Option Filename  Type Description
 
   -fnvt.mdp  Inputgrompp input file with MD parameters
  -po  mdout.mdp  Output   grompp input file with MD parameters
   -c em.gro  InputStructure file: gro g96 pdb tpr etc.
   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
   -n  index.ndx  Input, Opt!  Index file
   -p  topol.top  InputTopology file
  -pp  processed.top  Output, Opt. Topology file
   -onvt.tpr  Output   Run input file: tpr tpb tpa
   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
   -e   ener.edr  Input, Opt.  Energy file

 Option   Type   Value   Description
 --
 -[no]h   bool   no  Print help info and quit
 -[no]version bool   no  Print version info and quit
 -niceint0   Set the nicelevel
 -[no]v   bool   no  Be loud and noisy
 -timereal   -1  Take frame at or first after this time.
 -[no]rmvsbds bool   yes Remove constant bonded interactions with
 virtual
 sites
 -maxwarn int0   Number of allowed warnings during input
 processing
 -[no]zerobool   no  Set parameters for bonded interactions without
 defaults to zero instead of generating an error
 -[no]renum   bool   yes Renumber atomtypes and minimize number of
 atomtypes

 Ignoring obsolete mdp entry 'title'

 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#

 ERROR 1 [file nvt.mdp]:
   With coulombtype = PME-Switch, rcoulomb must be = rlist

 Generated 279 of the 1225 non-bonded parameter combinations
 Excluding 3 bonded neighbours molecule type 'Protein'
 turning all bonds into constraints...
 Excluding 3 bonded neighbours molecule type 'UNT'
 turning all bonds into constraints...
 Excluding 2 bonded neighbours molecule type 'SOL'
 turning all bonds into constraints...
 Excluding 1 bonded neighbours molecule type 'CL'
 turning all bonds into constraints...
 Setting gen_seed to 3507
 Velocities were taken from a Maxwell distribution at 300 K

 ---
 Program grompp, VERSION 4.5.3
 Source code file: grompp.c, line: 1356

 Fatal error:
 There was 1 error in input file(s)
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 Yeah, a Wuzz, Or a Jerk (F. Black)
  With Best Regards.

 Mr.Manoj Damale,
 M.S. Pharma (Pharmacoinformatics) NIPER,
 Kolkata, West Bengal State,
 India.
 --
 Gromacs Users mailing list

 * Please search the archive at
 

[gmx-users] Gromacs Error

[manoj damale]

Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for 
equlibriation in nvt.mdp file

mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p 
topol.top -n index.ndx -o nvt.tpr 
 :-)  G  R  O  M  A  C  S  (-:

   GRowing Old MAkes el Chrono Sweat

    :-)  VERSION 4.5.3  (-:

    Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
    Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
    Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
    Copyright (c) 2001-2010, The GROMACS development team at
    Uppsala University  The Royal Institute of Technology, Sweden.
    check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

    :-)  grompp  (-:

Option Filename  Type Description

  -f    nvt.mdp  Input    grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c em.gro  Input    Structure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt!  Index file
  -p  topol.top  Input    Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o    nvt.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-nice    int    0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-time    real   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
    sites
-maxwarn int    0   Number of allowed warnings during input processing
-[no]zero    bool   no  Set parameters for bonded interactions without
    defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
    atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#

ERROR 1 [file nvt.mdp]:
  With coulombtype = PME-Switch, rcoulomb must be = rlist

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'UNT'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to 3507
Velocities were taken from a Maxwell distribution at 300 K

---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Yeah, a Wuzz, Or a Jerk (F. Black)
 With Best Regards.

Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West Bengal State,
India.
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Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Gromacs error regarding default gromos bond type and angle type

[Negar Parvizi]

Dear Gromacs users
we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial).

This pdf file contains two cofactors including TPF and HEM. Our next step is to 
dock some antifungal drugs to this protein which is cytochrome of the fungi.
As the TPF was not located in the active site and due to the lack of topology 
informtaion for this cofactor in gromos force fields, we omitted the TPF .
Then we performed pdb2gmx on the protein along with the HEM cofactor. The 
pdb2gmx did not give error, so we were satisfied with the topology file.

But when in the step of adding ions, we performed grommp command to get the 
ions.tpr file, we faced with 7 errors:

these errors were saying that there are not gromos default bond type or angle 
type or dihedral type for specified lines in the topology file.

I checked the atom numbers that were present in those bonds, angles and 
dihedrals and came to the conclusion hat all of them contain (Fe) atom which is 
present in the HEM cofactor.

It seems that pdb2gmx command is not able to specify gromos default bond type 
or angle type whenever Fe is there.

Now please guide us to solve the problem.
what should I put in the vacancy spaces for these bond type or angle types. I 
mean what (gb_? or ga_?)
and why the pdb2gmx did not gave error???

Thanks alot



-- 
Dr. Delara Mohammad-Aghaie
Assistant Professor of Physical Chemistry
Department of Chemistry
Shiraz University of Technology
Shiraz
Iran



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[gmx-users] gromacs error

[Yaser Hosseini]

hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:


gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
 Command 'gcx' from package 'gcx' (universe)
 Command 'ngmx' from package 'gromacs' (universe)
 Command 'gm' from package 'graphicsmagick' (universe)
 Command 'gmt' from package 'libgenome-perl' (universe)
gmx: command not found


and other problem :

solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
solvate: command not found

thank you for your help.
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Re: [gmx-users] gromacs error

[Justin Lemkul]

On 9/22/14 10:14 AM, Yaser Hosseini wrote:

hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:


gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
  Command 'gcx' from package 'gcx' (universe)
  Command 'ngmx' from package 'gromacs' (universe)
  Command 'gm' from package 'graphicsmagick' (universe)
  Command 'gmt' from package 'libgenome-perl' (universe)
gmx: command not found



You haven't configured your environment properly.

http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation



and other problem :

solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
solvate: command not found



That's not a valid command.  gmx solvate is, if you follow the instructions 
above.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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* Please search the archive at 
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Re: [gmx-users] gromacs error

[Urszula Uciechowska]

How should I correct the input file?

Urszula Uciechowska


 On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:
 Dear Gromacs users,


 I tried to run coarse grained MD however after a few steps I got:
 Step 39, time 0.78 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
10457  10459   89.80.3107   0.8288  0.3100
10459  10463   90.30.3075   1.0108  0.3100
10463  10467   90.60.3084   0.8774  0.3100
10467  10469   81.10.3103   0.3823  0.3100
10469  10471   90.30.3121   0.1885  0.3100
 Wrote pdb files with previous and current coordinates

 Step 40, time 0.8 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 165002.767686, max 10334958.00 (between atoms 10457 and 10459)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
10443  10445   30.10.3100   0.3581  0.3100
10445  10447  102.20.3102 266.6146  0.3100
10447  10450   59.30.3100 624.1382  0.3100
10450  10452  101.40.3105 5390.4609  0.3100
10452  10454   87.90.3083 104154.3047  0.3100
10454  10457   83.90.3497 439143.5312  0.3100
10457  10459   87.50.8288 3203837.2500  0.3100
10459  10463   87.81.0108 2960821.2500  0.3100
10463  10467   95.20.8774 763857.8125  0.3100
10467  10469   95.50.3823 195859.2656  0.3100
10469  10471  104.30.1885 43565.4141  0.3100
10471  10473   90.30.3534 7857.3394  0.3100
10473  10475  105.50.3125  57.7529  0.3100
10475  10477   90.00.3099   0.3849  0.3100
10477  10480   32.40.3101   0.3647  0.3100
 Wrote pdb files with previous and current coordinates
 mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
 mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
 mpiexec: kill_others_now: alarm went off, killing all other tasks.
 mpiexec: kill_tasks: killing all tasks.
 mpiexec: process_kill_event: evt 10 task 1 on wn350.
 mpiexec: process_kill_event: evt 12 task 3 on wn501.
 mpiexec: process_kill_event: evt 11 task 2 on wn350.
 mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
 mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
 mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
 mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
 mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).

 in log file last line is:

 Constraining the starting coordinates (step 0)

 Constraining the coordinates at t0-dt (step 0)
 RMS relative constraint deviation after constraining: 4.04e-06
 Initial temperature: 1.8161e-07 K

 Started mdrun on node 0 Wed Jul 30 10:39:50 2014

 Step   Time Lambda
00.00.0

 Grid: 42 x 42 x 42 cells
 Energies (kJ/mol)
 Bond   G96AngleProper Dih.  Improper Dih.LJ
 (SR)
  6.24872e+031.47844e+041.75778e+034.11810e+02
 -2.32179e+07
 Coulomb (SR) Position Rest.  PotentialKinetic En.   Total
 Energy
 -4.49776e+032.00073e-01   -2.31992e+071.44043e+01
 -2.31992e+07
  Temperature Pressure (bar)   Constr. rmsd
  1.55259e-03   -1.41563e+035.56533e-06

 my input file:

 define   =  -DPOSRES
 dt   =  0.02
 nsteps   =  25000
 nstxout  =  0
 nstvout  =  0
 nstlog   =  100
 nstxtcout=  100
 xtc-precision=  10
 rlist=  1.4
 coulombtype  =  shift
 rcoulomb =  1.2
 epsilon_r=  15
 vdw-type =  shift
 rvdw-switch  =  0.9
 rvdw =  1.2
 tcoupl   =  v-rescale
 tc-grps  =  Protein W
 tau-t=  1.0 1.0
 ref-t=  300 300
 Pcoupl   =  Berendsen
 Pcoupltype   =  isotropic
 tau-p=  12.0
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  com

What is wrong here?


 Likely this:

 Initial temperature: 1.8161e-07 K

 You haven't generated any velocities, so your system is effectively
 frozen, and
 you're simultaneously applying a thermostat and barostat, which probably
 cause
 your velocities to go absolutely insane, blowing up the system.

 Generate velocities at the desired temperature and equilibrate gently.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs 

Re: [gmx-users] gromacs error

[Justin Lemkul]

On 7/31/14, 8:16 AM, Urszula Uciechowska wrote:

How should I correct the input file?



http://manual.gromacs.org/online/mdp_opt.html#vel

And get your hands on some suitable tutorial material; proper use of these 
settings is routine.


-Justin


Urszula Uciechowska



On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:

Dear Gromacs users,


I tried to run coarse grained MD however after a few steps I got:
Step 39, time 0.78 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
10457  10459   89.80.3107   0.8288  0.3100
10459  10463   90.30.3075   1.0108  0.3100
10463  10467   90.60.3084   0.8774  0.3100
10467  10469   81.10.3103   0.3823  0.3100
10469  10471   90.30.3121   0.1885  0.3100
Wrote pdb files with previous and current coordinates

Step 40, time 0.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 165002.767686, max 10334958.00 (between atoms 10457 and 10459)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
10443  10445   30.10.3100   0.3581  0.3100
10445  10447  102.20.3102 266.6146  0.3100
10447  10450   59.30.3100 624.1382  0.3100
10450  10452  101.40.3105 5390.4609  0.3100
10452  10454   87.90.3083 104154.3047  0.3100
10454  10457   83.90.3497 439143.5312  0.3100
10457  10459   87.50.8288 3203837.2500  0.3100
10459  10463   87.81.0108 2960821.2500  0.3100
10463  10467   95.20.8774 763857.8125  0.3100
10467  10469   95.50.3823 195859.2656  0.3100
10469  10471  104.30.1885 43565.4141  0.3100
10471  10473   90.30.3534 7857.3394  0.3100
10473  10475  105.50.3125  57.7529  0.3100
10475  10477   90.00.3099   0.3849  0.3100
10477  10480   32.40.3101   0.3647  0.3100
Wrote pdb files with previous and current coordinates
mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
mpiexec: kill_others_now: alarm went off, killing all other tasks.
mpiexec: kill_tasks: killing all tasks.
mpiexec: process_kill_event: evt 10 task 1 on wn350.
mpiexec: process_kill_event: evt 12 task 3 on wn501.
mpiexec: process_kill_event: evt 11 task 2 on wn350.
mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).

in log file last line is:

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.04e-06
Initial temperature: 1.8161e-07 K

Started mdrun on node 0 Wed Jul 30 10:39:50 2014

 Step   Time Lambda
00.00.0

Grid: 42 x 42 x 42 cells
 Energies (kJ/mol)
 Bond   G96AngleProper Dih.  Improper Dih.LJ
(SR)
  6.24872e+031.47844e+041.75778e+034.11810e+02
-2.32179e+07
 Coulomb (SR) Position Rest.  PotentialKinetic En.   Total
Energy
 -4.49776e+032.00073e-01   -2.31992e+071.44043e+01
-2.31992e+07
  Temperature Pressure (bar)   Constr. rmsd
  1.55259e-03   -1.41563e+035.56533e-06

my input file:

define   =  -DPOSRES
dt   =  0.02
nsteps   =  25000
nstxout  =  0
nstvout  =  0
nstlog   =  100
nstxtcout=  100
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein W
tau-t=  1.0 1.0
ref-t=  300 300
Pcoupl   =  Berendsen
Pcoupltype   =  isotropic
tau-p=  12.0
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  com

What is wrong here?



Likely this:

Initial temperature: 1.8161e-07 K

You haven't generated any velocities, so your system is effectively
frozen, and
you're simultaneously applying a thermostat and barostat, which probably
cause
your velocities to go absolutely insane, blowing up the system.

Generate velocities at the desired temperature and equilibrate gently.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

Re: [gmx-users] gromacs error

[Urszula Uciechowska]

Can anyone help me with this error file? I did not get the log file...


Back Off! I just backed up md.log to ./#md.log.5#
Reading file md10ns-2.tpr, VERSION 4.5.3 (single precision)

Reading checkpoint file md10ns.cpt generated: Mon Jul 21 20:45:14 2014


Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical,
 see the log file for details.


Will use 18 particle-particle and 14 PME only nodes
This is a guess, check the performance at the end of the log file
Making 2D domain decomposition 2 x 9 x 1

Back Off! I just backed up traj.trr to ./#traj.trr.5#

Back Off! I just backed up traj.xtc to ./#traj.xtc.5#

Back Off! I just backed up ener.edr to ./#ener.edr.5#

WARNING: This run will generate roughly 5776 Mb of data

starting mdrun 'Protein in water'
1000 steps,  2.0 ps (continuing from step 500,  1.0 ps).

NOTE: Turning on dynamic load balancing


Writing final coordinates.

Back Off! I just backed up confout.gro to ./#confout.gro.1#

 Average load imbalance: 13.5 %
 Part of the total run time spent waiting due to load imbalance: 3.8 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X
0 % Y 98 %
 Average PME mesh/force load: 0.833
 Part of the total run time spent waiting due to PP/PME imbalance: 3.4 %


my input file:

 7.3.3 Run Control
integrator  = md; md integrator
tinit   = 0 ; [ps] starting time for run
dt  = 0.002 ; [ps] time step for
integration
nsteps  = 500   ; maximum number of steps
to integrate, 0.002 * 2,500,000 = 5,000 ps
comm_mode   = Linear; remove center of mass
translation
nstcomm = 1 ; [steps] frequency of
mass motion removal
comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal
; 7.3.8 Output Control
nstxout = 250   ; [steps] freq to write
coordinates to trajectory
nstvout = 250   ; [steps] freq to write velocities
to trajectory
nstfout = 250   ; [steps] freq to write forces to
trajectory
nstlog  = 100   ; [steps] freq to write energies
to log file
nstenergy   = 500   ; [steps] freq to write energies
to energy file
nstxtcout   = 500   ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision   = 1000  ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc trajectory
energygrps  = System; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions
rlist   = 0.8   ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 0.8   ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype = cut-off   ; twin-range cut-off with rlist
where rvdw = rlist
rvdw= 0.8   ; [nm] distance for LJ cut-off
DispCorr= EnerPres  ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl  = v-rescale ; temperature
coupling with Nose-Hoover ensemble
tc_grps = ProteinNon-Protein; groups to couple
seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 310310; [K] reference
temperature for coupling

; 7.3.15 Pressure Coupling
pcoupl  = parrinello-rahman ; pressure coupling where
box vectors are variable
pcoupltype  = isotropic ; pressure coupling in
x-y-z directions
tau_p   = 2.0   ; [ps] time constant for
coupling
compressibility = 4.5e-5; [bar^-1] compressibility
ref_p   = 1.0   ; [bar] reference pressure
for coupling

; 7.3.17 Velocity Generation
gen_vel = no; velocity generation turned off

; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS 

Re: [gmx-users] gromacs error

[Justin Lemkul]

On 7/31/14, 8:36 AM, Urszula Uciechowska wrote:

Can anyone help me with this error file? I did not get the log file...



There is no error here.  I assume this is what is concerning:


Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical,
  see the log file for details.



This means you're either changing Gromacs versions between runs (bad idea) or 
changing something about how the run is parallelized.  As the message cautions, 
this can lead to differences in behavior that would not have occurred if what 
you were doing was consistent.  Absent any version or command information, 
there's little else to say.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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