Re: [gmx-users] Fwd: how to get .mdp files

[Tasneem Kausar]

mdp file is parameter file for md simulations.
You need to copy if you want to use the parameters used in the tutorial.
You can also change that parameter according to your use and need.

On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa  wrote:

> -- Forwarded message --
> From: "neelam wafa" 
> Date: 17 Feb 2018 00:57
> Subject: how to get .mdp files
> To: 
> Cc:
>
> Hi
> I am new to this list. I have run the gromacs tutorial ' lysosime in
> water'. now i have to run a protein ligand simmulation. But i am confused
> about how to generate .mdp files as in tutorial they have used five .mdp
> files which are to be downloaded from bevanlab.biochem. These are ions.mdp,
> em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these
> have to be generated with aome software according to the protein and
> ligand.
>
> Thanks in advance.
>
> Regards
> Neelam
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[gmx-users] Fwd: how to get .mdp files

[neelam wafa]

-- Forwarded message --
From: "neelam wafa" 
Date: 17 Feb 2018 00:57
Subject: how to get .mdp files
To: 
Cc:

Hi
I am new to this list. I have run the gromacs tutorial ' lysosime in
water'. now i have to run a protein ligand simmulation. But i am confused
about how to generate .mdp files as in tutorial they have used five .mdp
files which are to be downloaded from bevanlab.biochem. These are ions.mdp,
em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these
have to be generated with aome software according to the protein and ligand.

Thanks in advance.

Regards
Neelam
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[gmx-users] Print neighbour list

[fabio trovato]

Hi,

I am trying to output the neighbor list calculated during a simulation. I
consulted the manual which says that DUMPNL is the env variable suited for
this purpose.

In my bash script I first set up:
export DUMPNL=10

and then run the simulation (GROMACS version 4.5.4).

I do not see any neighbor list printed in my md.log file. What am I doing
wrong? Does anyone knows how to solve this?

Thank you,
Fabio
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[gmx-users] ion channel in lipid bilayer

[alex rayevsky]

Hi all!

I have a question concerning immersion of the ion channel (four subunits
with extracellular domains and a bundles of helixes)  into the lipid
bilayer. 6 years ago I used some tutorial or mailing lists, which described
the way from KALP15 tutor. With CCR5 model there were no problems at all.
Now I have a not 'cylindric'  protein with a complex shape and overhanging
domains.
the forcefield is CHARMM36, lipid type - POPG.

I tried Membrane builder, but couldn't orient the plane of the membrane by
changing XYZ principles many times in different combinations.. Thus I used
a slightly modified KALP15 method (other .itps, lipids and water
molecules).  First of all after pdb2gmx for protein a series of topologies
were generated with identifiers in the name, as it was assigned in each
chain. However editconf produced a new pdb from the outpu gro without any
ID or terminators for the chains, in Pymol it is represented with a
tetramer entirely highlithing if a single chain is selected (maybe it is a
reason of faults at later stages).

Well, it works fine until the perl script execution. Beside some problems
with the output (system_inflated.gro was corrupted, but I repaired it with
simple python scripting and got a pretty protein in the center of rare
molecules, which looks reliable enough) I started to compact the bilayer to
rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
execution - the distance between nearest lipids was about 16A, however, the
layer was really holey. At the same time the protein was not surrounded
from all sides. But if I try to put lipids closely one to other, they are
simultaneously penetrate the protein body.

Is it the correct method for such kind of simmulations? Could I increase
the number of POPG molecules after getting inflated.gro file with scaled up
bilayer (the initial step for tightning) before scaling iterations? I can
do it manually by copy of the layer (all lipid coordinates) and its
rotation around Y axis in any soft to enlarge the number of molecules in
the cell (even 200 mols is more than 128). Of course I will make changes in
a topology file. It seems, that I will obtain a fully wrapped protein
without anxiety about clashes or presure in cavities...

What do You think? Thank You in advance!



*Nemo me impune lacessit*
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Re: [gmx-users] Problems with trjconv

[Justin Lemkul]

On 2/16/18 3:00 PM, Poncho Arvayo Zatarain wrote:

Where shud i see the answer Justin? Please tell me



Like any other post, in your email.

-Justin



De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: viernes, 16 de febrero de 2018 11:50 a. m.
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] Problems with trjconv



On 2/16/18 2:35 PM, Poncho Arvayo Zatarain wrote:

Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is 
inverted, the water is in the middle and the lipid tails are outside. How can i 
flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr 
-n index -o file.gro -pbc whole but nothing happens. In index i use option 
System. What can i do to flip the bilayer? should i use lipid and water options 
in index?

I answered this earlier this morning. Please try what I suggested.

-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
Justin Lemkul
www.biochem.vt.edu




==

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--
==

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] GPU problem with running gromacs.2018

[Mark Abraham]

Hi,

You can upload a log file to a file-sharing service and share the link :-)

Mark

On Fri, Feb 16, 2018 at 8:22 PM Osmany Guirola Cruz <
osmany.guir...@biocomp.cigb.edu.cu> wrote:

> Hi,
> When I send the full log  I received this mail from the list.
>
> -
>
>
> Your mail to 'gromacs.org_gmx-users' with the subject
>
> Re: [gmx-users] GPU problem with running gromacs.2018
>
> Is being held until the list moderator can review it for approval.
>
> The reason it is being held:
>
> Message body is too big: 60010 bytes with a limit of 50 KB
>
> Either the message will get posted to the list, or you will receive
> notification of the moderator's decision.  If you would like to cancel
> this posting, please visit the following URL:
>
> https://maillist.sys.kth.se/mailman/confirm/gromacs.org_gmx-users/1
> 29a1575b806c54484b39d65032d5862b41be235
> 
>
>
>
> --
>
>
>
>
>
> -Original Message-
> From: Szilárd Páll 
> Reply-to: gmx-us...@gromacs.org
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] GPU problem with running gromacs.2018
> Date: Fri, 16 Feb 2018 20:06:05 +0100
>
> Hi,
>
> Indeed, this is an issue introduced in the 2018 release which aborts
> mdrun if an error is encountered during GPU detection; My first guess
> is that one of your GPUs is in exclusive or prohibited mode. You can
> use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES
> environment variable.
>
> BTW, what you shared is  not your full log! It would have been (and
> will be in the future) helpful if you actually shared the _full_ log
> file so we get all information not just what you find useful to paste
> in your reply; in this particular case seeing the hardware detection
> report would have helped a bit.
>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz
>  wrote:
> > This is the output with gromacs 2018 and cuda 9
> > -
> > --Program: gmx
> > mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
> > (line 735)Function:void findGpus(gmx_gpu_info_t*)
> > Assertion failed:Condition: cudaSuccess ==
> > cudaPeekAtLastError()Should
> > be cudaSuccess
> > For more information and tips for troubleshooting, please check the
> > GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> > --
> > -
> >
> > and this is the log
> > Log file opened on Fri Feb 16 07:49:19 2018Host: draco  pid:
> > 20855  rank ID: 0  number of ranks:  1   :-)
> > GROMACS - gmx mdrun, 2018 (-:
> > GROMACS is written by: Emile
> > Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > BjelkmarAldert van Buuren   Rudi van Drunen Anton
> > FeenstraGerrit Groenhof   Christoph Junghans   Anca
> > HamuraruVincent Hindriksen Dimitrios KarkoulisPeter
> > KassonJiri Kraus  Carsten Kutzner  Per Larsson
> > Justin A. LemkulViveca LindahlMagnus Lundborg   Pieter
> > MeulenhoffErik Marklund  Teemu Murtola   Szilard
> > Pall   Sander Pronk  Roland Schulz Alexey
> > Shvetsov Michael Shirts Alfons Sijbers Peter
> > TielemanTeemu 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) 2001-2017, The GROMACS development team
> > atUppsala University, Stockholm University andthe 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
> > itunder
> > the terms of the GNU Lesser General Public Licenseas published by the
> > Free Software Foundation; either version 2.1of the License, or (at
> > your
> > option) any later version.
> > GROMACS:  gmx mdrun, version
> > 2018Executable:   /usr/local/gromacs/bin/gmxData
> > prefix:  /usr/local/gromacsWorking
> > dir:  /home/osmany/Downloads/RASCommand line:  gmx mdrun -deffnm md
> > GROMACS version:2018Precision:  singleMemory
> > model:   64 bitMPI library:thread_mpiOpenMP
> > support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU
> > support:CUDASIMD instructions:  SSE4.1FFT
> > library:fftw-
> > 3.3.7-sse2-avxRDTSCP usage:   disabledTNG
> > support:enabledHwloc support:  hwloc-1.11.6Tracing
> > support:disabledBuilt on:   2018-02-14 14:05:11Built
> > by:   osmany@draco [CMAKE]Build OS/arch:  Linux 4.14.0-3-
> > amd64 

Re: [gmx-users] Problems with trjconv

[Justin Lemkul]

On 2/16/18 2:35 PM, Poncho Arvayo Zatarain wrote:


Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is 
inverted, the water is in the middle and the lipid tails are outside. How can i 
flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr 
-n index -o file.gro -pbc whole but nothing happens. In index i use option 
System. What can i do to flip the bilayer? should i use lipid and water options 
in index?


I answered this earlier this morning. Please try what I suggested.

-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] Problems with trjconv

[Poncho Arvayo Zatarain]

Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is 
inverted, the water is in the middle and the lipid tails are outside. How can i 
flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr 
-n index -o file.gro -pbc whole but nothing happens. In index i use option 
System. What can i do to flip the bilayer? should i use lipid and water options 
in index?
-- 
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] GPU problem with running gromacs.2018

[Osmany Guirola Cruz]

Hi,
When I send the full log  I received this mail from the list.

-


Your mail to 'gromacs.org_gmx-users' with the subject

Re: [gmx-users] GPU problem with running gromacs.2018

Is being held until the list moderator can review it for approval.

The reason it is being held:

Message body is too big: 60010 bytes with a limit of 50 KB

Either the message will get posted to the list, or you will receive
notification of the moderator's decision.  If you would like to cancel
this posting, please visit the following URL:

https://maillist.sys.kth.se/mailman/confirm/gromacs.org_gmx-users/1
29a1575b806c54484b39d65032d5862b41be235



--





-Original Message-
From: Szilárd Páll 
Reply-to: gmx-us...@gromacs.org
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] GPU problem with running gromacs.2018
Date: Fri, 16 Feb 2018 20:06:05 +0100

Hi,

Indeed, this is an issue introduced in the 2018 release which aborts
mdrun if an error is encountered during GPU detection; My first guess
is that one of your GPUs is in exclusive or prohibited mode. You can
use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES
environment variable.

BTW, what you shared is  not your full log! It would have been (and
will be in the future) helpful if you actually shared the _full_ log
file so we get all information not just what you find useful to paste
in your reply; in this particular case seeing the hardware detection
report would have helped a bit.

Cheers,
--
Szilárd


On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz
 wrote:
> This is the output with gromacs 2018 and cuda 9
> -
> --Program: gmx
> mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
> (line 735)Function:void findGpus(gmx_gpu_info_t*)
> Assertion failed:Condition: cudaSuccess ==
> cudaPeekAtLastError()Should
> be cudaSuccess
> For more information and tips for troubleshooting, please check the
> GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> --
> -
> 
> and this is the log
> Log file opened on Fri Feb 16 07:49:19 2018Host: draco  pid:
> 20855  rank ID: 0  number of ranks:  1   :-)
> GROMACS - gmx mdrun, 2018 (-:
> GROMACS is written by: Emile
> Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> BjelkmarAldert van Buuren   Rudi van Drunen Anton
> FeenstraGerrit Groenhof   Christoph Junghans   Anca
> HamuraruVincent Hindriksen Dimitrios KarkoulisPeter
> KassonJiri Kraus  Carsten Kutzner  Per Larsson
> Justin A. LemkulViveca LindahlMagnus Lundborg   Pieter
> MeulenhoffErik Marklund  Teemu Murtola   Szilard
> Pall   Sander Pronk  Roland Schulz Alexey
> Shvetsov Michael Shirts Alfons Sijbers Peter
> TielemanTeemu 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) 2001-2017, The GROMACS development team
> atUppsala University, Stockholm University andthe 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
> itunder
> the terms of the GNU Lesser General Public Licenseas published by the
> Free Software Foundation; either version 2.1of the License, or (at
> your
> option) any later version.
> GROMACS:  gmx mdrun, version
> 2018Executable:   /usr/local/gromacs/bin/gmxData
> prefix:  /usr/local/gromacsWorking
> dir:  /home/osmany/Downloads/RASCommand line:  gmx mdrun -deffnm md
> GROMACS version:2018Precision:  singleMemory
> model:   64 bitMPI library:thread_mpiOpenMP
> support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU
> support:CUDASIMD instructions:  SSE4.1FFT
> library:fftw-
> 3.3.7-sse2-avxRDTSCP usage:   disabledTNG
> support:enabledHwloc support:  hwloc-1.11.6Tracing
> support:disabledBuilt on:   2018-02-14 14:05:11Built
> by:   osmany@draco [CMAKE]Build OS/arch:  Linux 4.14.0-3-
> amd64 x86_64Build CPU vendor:   IntelBuild CPU brand:Intel(R)
> Core(TM)2 Quad CPUQ9650  @ 3.00GHzBuild CPU family:   6   Model:
> 23   Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel
> lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C
> compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags:-
> msse4.1 -O3 -DNDEBUG -funroll-all-loops -fexcess-
> precision=fast  C++ compiler:   /usr/bin/g++-6 GNU 6.4.0C++
> compiler flags:  -msse4.1-std=c++11   -O3 -DNDEBUG -funroll-all-

Re: [gmx-users] GPU problem with running gromacs.2018

[Szilárd Páll]

Hi,

Indeed, this is an issue introduced in the 2018 release which aborts
mdrun if an error is encountered during GPU detection; My first guess
is that one of your GPUs is in exclusive or prohibited mode. You can
use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES
environment variable.

BTW, what you shared is  not your full log! It would have been (and
will be in the future) helpful if you actually shared the _full_ log
file so we get all information not just what you find useful to paste
in your reply; in this particular case seeing the hardware detection
report would have helped a bit.

Cheers,
--
Szilárd


On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz
 wrote:
> This is the output with gromacs 2018 and cuda 9
> ---Program: gmx
> mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
> (line 735)Function:void findGpus(gmx_gpu_info_t*)
> Assertion failed:Condition: cudaSuccess == cudaPeekAtLastError()Should
> be cudaSuccess
> For more information and tips for troubleshooting, please check the
> GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--
> -
>
> and this is the log
> Log file opened on Fri Feb 16 07:49:19 2018Host: draco  pid:
> 20855  rank ID: 0  number of ranks:  1   :-)
> GROMACS - gmx mdrun, 2018 (-:
> GROMACS is written by: Emile
> Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> BjelkmarAldert van Buuren   Rudi van Drunen Anton
> FeenstraGerrit Groenhof   Christoph Junghans   Anca
> HamuraruVincent Hindriksen Dimitrios KarkoulisPeter
> KassonJiri Kraus  Carsten Kutzner  Per Larsson
> Justin A. LemkulViveca LindahlMagnus Lundborg   Pieter
> MeulenhoffErik Marklund  Teemu Murtola   Szilard
> Pall   Sander Pronk  Roland Schulz Alexey
> Shvetsov Michael Shirts Alfons Sijbers Peter
> TielemanTeemu 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) 2001-2017, The GROMACS development team
> atUppsala University, Stockholm University andthe 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 itunder
> the terms of the GNU Lesser General Public Licenseas published by the
> Free Software Foundation; either version 2.1of the License, or (at your
> option) any later version.
> GROMACS:  gmx mdrun, version
> 2018Executable:   /usr/local/gromacs/bin/gmxData
> prefix:  /usr/local/gromacsWorking
> dir:  /home/osmany/Downloads/RASCommand line:  gmx mdrun -deffnm md
> GROMACS version:2018Precision:  singleMemory
> model:   64 bitMPI library:thread_mpiOpenMP
> support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU
> support:CUDASIMD instructions:  SSE4.1FFT library:fftw-
> 3.3.7-sse2-avxRDTSCP usage:   disabledTNG
> support:enabledHwloc support:  hwloc-1.11.6Tracing
> support:disabledBuilt on:   2018-02-14 14:05:11Built
> by:   osmany@draco [CMAKE]Build OS/arch:  Linux 4.14.0-3-
> amd64 x86_64Build CPU vendor:   IntelBuild CPU brand:Intel(R)
> Core(TM)2 Quad CPUQ9650  @ 3.00GHzBuild CPU family:   6   Model:
> 23   Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel
> lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C
> compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags:-
> msse4.1 -O3 -DNDEBUG -funroll-all-loops -fexcess-
> precision=fast  C++ compiler:   /usr/bin/g++-6 GNU 6.4.0C++
> compiler flags:  -msse4.1-std=c++11   -O3 -DNDEBUG -funroll-all-
> loops -fexcess-precision=fast  CUDA compiler:  /usr/lib/nvidia-
> cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright
> (c) 2005-2017 NVIDIA Corporation;Built on
> Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0,
> V9.0.176CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-
> gencode;arch=compute_35,code=sm_35;-
> gencode;arch=compute_37,code=sm_37;-
> gencode;arch=compute_50,code=sm_50;-
> gencode;arch=compute_52,code=sm_52;-
> gencode;arch=compute_60,code=sm_60;-
> gencode;arch=compute_61,code=sm_61;-
> gencode;arch=compute_70,code=sm_70;-
> gencode;arch=compute_70,code=compute_70;-use_fast_math;-
> D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all-
> loops;-fexcess-precision=fast;CUDA driver:9.0CUDA
> runtime:   9.0
> --
>
>
> Osmany
>
>
>
>
>
> -Original Message-From: Szilárd Páll Re
> ply-to: 

[gmx-users] GROMACS 2016.5 released

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 2016.5 is available!

This release fixes several minor issues found since 2016.4. It incorporates
all the fixes found in the 5.1.5 release. We encourage all users of the
2016 series to update to 2016.5. Please see the link to the release notes
below for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016.5.tar.gz
http://manual.gromacs.org/documentation/2016.5/index.html (including
installation guide, user guide, reference manual)
http://manual.gromacs.org/documentation/2016.5/ReleaseNotes/index.html
http://gerrit.gromacs.org/download/regressiontests-2016.5.tar.gz

Happy simulating!

Mark Abraham
GROMACS Development Manager
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Re: [gmx-users] GPU problem with running gromacs.2018

[Osmany Guirola Cruz]

This is the output with gromacs 2018 and cuda 9
---Program: gmx
mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
(line 735)Function:void findGpus(gmx_gpu_info_t*)
Assertion failed:Condition: cudaSuccess == cudaPeekAtLastError()Should
be cudaSuccess
For more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--
-

and this is the log
Log file opened on Fri Feb 16 07:49:19 2018Host: draco  pid:
20855  rank ID: 0  number of ranks:  1   :-)
GROMACS - gmx mdrun, 2018 (-:
GROMACS is written by: Emile
Apol  Rossen Apostolov  Herman J.C. BerendsenPar
BjelkmarAldert van Buuren   Rudi van Drunen Anton
FeenstraGerrit Groenhof   Christoph Junghans   Anca
HamuraruVincent Hindriksen Dimitrios KarkoulisPeter
KassonJiri Kraus  Carsten Kutzner  Per Larsson 
Justin A. LemkulViveca LindahlMagnus Lundborg   Pieter
MeulenhoffErik Marklund  Teemu Murtola   Szilard
Pall   Sander Pronk  Roland Schulz Alexey
Shvetsov Michael Shirts Alfons Sijbers Peter
TielemanTeemu 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) 2001-2017, The GROMACS development team
atUppsala University, Stockholm University andthe 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 itunder
the terms of the GNU Lesser General Public Licenseas published by the
Free Software Foundation; either version 2.1of the License, or (at your
option) any later version.
GROMACS:  gmx mdrun, version
2018Executable:   /usr/local/gromacs/bin/gmxData
prefix:  /usr/local/gromacsWorking
dir:  /home/osmany/Downloads/RASCommand line:  gmx mdrun -deffnm md
GROMACS version:2018Precision:  singleMemory
model:   64 bitMPI library:thread_mpiOpenMP
support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU
support:CUDASIMD instructions:  SSE4.1FFT library:fftw-
3.3.7-sse2-avxRDTSCP usage:   disabledTNG
support:enabledHwloc support:  hwloc-1.11.6Tracing
support:disabledBuilt on:   2018-02-14 14:05:11Built
by:   osmany@draco [CMAKE]Build OS/arch:  Linux 4.14.0-3-
amd64 x86_64Build CPU vendor:   IntelBuild CPU brand:Intel(R)
Core(TM)2 Quad CPUQ9650  @ 3.00GHzBuild CPU family:   6   Model:
23   Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel
lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C
compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags:-
msse4.1 -O3 -DNDEBUG -funroll-all-loops -fexcess-
precision=fast  C++ compiler:   /usr/bin/g++-6 GNU 6.4.0C++
compiler flags:  -msse4.1-std=c++11   -O3 -DNDEBUG -funroll-all-
loops -fexcess-precision=fast  CUDA compiler:  /usr/lib/nvidia-
cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright
(c) 2005-2017 NVIDIA Corporation;Built on
Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0,
V9.0.176CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-
gencode;arch=compute_35,code=sm_35;-
gencode;arch=compute_37,code=sm_37;-
gencode;arch=compute_50,code=sm_50;-
gencode;arch=compute_52,code=sm_52;-
gencode;arch=compute_60,code=sm_60;-
gencode;arch=compute_61,code=sm_61;-
gencode;arch=compute_70,code=sm_70;-
gencode;arch=compute_70,code=compute_70;-use_fast_math;-
D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all-
loops;-fexcess-precision=fast;CUDA driver:9.0CUDA
runtime:   9.0
--


Osmany





-Original Message-From: Szilárd Páll Re
ply-to: gmx-users@gromacs.orgTo: Discussion list for GROMACS users Subject: Re: [gmx-users] GPU problem with running
gromacs.2018Date: Thu, 15 Feb 2018 18:23:05 +0100
Please provide a full log file output.--Szilárd

On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz wrote:
> Hi
> 
> I am having problems running mdrun command compiled with GPU
> support(cuda 9.0).
> here is  the output of the mdrun command
> 
> 
> Using 1 MPI thread
> Using 4 OpenMP threads
> 
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 1 PP rank in this node: 0
> 
> 
> WARNING: Just caught a previously occurred CUDA error (no kernel
> image
> is available for execution on the device), will try to continue.
> 
> 
> ---
> Program: gmx mdrun, version 2016.4
> Source file: 

Re: [gmx-users] Flip a bilayer

[Justin Lemkul]

On 2/15/18 12:38 PM, Poncho Arvayo Zatarain wrote:

Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in 
vmd, is inverted, the water is in the middle and the lipid tails are outside. 
How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s 
file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use 
option System. What can i do to flip the bilayer? should i use lipid and water 
options in index?
Use the -trans option on the lipids to set a translation equal to half 
the box along the membrane normal.


-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] Secondary structure propensity.

[Justin Lemkul]

On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:

Hello,

I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.


Only indirectly, but scount.xvg has all that is needed, the number of 
residues in a given secondary structure as a function of time. From 
that, percentage over time is a trivial scripting task, [(# in SS) / (# 
of residues)]*100.


-Justin


Regards,

S. Borkotoky

On Fri, Feb 16, 2018 at 1:30 PM, Sundari  wrote:


Dear gromacs users,

can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.

I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or something
different?

Thank you in advance..
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--
==

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] 2018 performance question

[Michael Brunsteiner]

hi
just installed gmx-2018 on a x86_64 PC with a Geforce GTX 780 and the 
cudasoftware directly from the nvidia webpage (didn't work using the debian 
nvidia packages)
output of lscpu is included below.
i find that:
1) 2018 is slightly faster (~5%) than 2016.2) both 2016 and 2018 use the GPU, 
but 2018 seems to use less CPU.
With 2016 using the "top" command i usually see that the CPU load is close to 
1200%(i have 6 cores, each two threads) while with 2018 this number is closer 
to around 400%(I guess this is because 2018 does PME on the GPU)
my question is: can i possibly further improve the performance of 2018 by1) 
somehow convincing gmx to use more CPU, or
2) run two instances of gmx on this one computer simultaneously??
thanks in advance for any feedback!
cheers,Michael



prompt> lscpuArchitecture:  x86_64
CPU op-mode(s):    32-bit, 64-bit
Byte Order:    Little Endian
CPU(s):    12
On-line CPU(s) list:   0-11
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s): 1
NUMA node(s):  1
Vendor ID: GenuineIntel
CPU family:    6
Model: 62
Model name:    Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
Stepping:  4
CPU MHz:   3399.898
CPU max MHz:   3900.
CPU min MHz:   1200.
BogoMIPS:  6799.79
Virtualization:    VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  12288K
NUMA node0 CPU(s): 0-11
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca 
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx 
pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 
ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer 
aes xsave avx f16c rdrand lahf_lm epb kaiser tpr_shadow vnmi flexpriority ept 
vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts


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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Hello,

I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.

Regards,

S. Borkotoky

On Fri, Feb 16, 2018 at 1:30 PM, Sundari  wrote:

> Dear gromacs users,
>
> can any one please tell me that how we get the secondary structure
> propensity or secondary structure content(%) as a function of simulation
> time.
>
> I used "gmx do_dssp" but it gives me number of residues forming the
> secondary structure vs simulation time. is it same thing or something
> different?
>
> Thank you in advance..
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Yours Sincerely,
--
*Dr. Subhomoi Borkotoky, Ph. D.*
DBT Research Associate,
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.


https://scholar.google.co.in/citations?user=bJz7GokJ=en
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[gmx-users] (no subject)

[Sundari]

Dear gromacs users,

can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.

I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or something
different?

Thank you in advance..
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[gmx-users] Secondary structure propensity.

[Sundari]

Dear gromacs users,

can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.

I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or something
different?

Thank you in advance..
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