date:20191208

[gmx-users] GROMACS for replica exchange - recommendation for the research papers

2019-12-08 Thread Gil Vernik

I managed to follow the tutorial on replica exchange by Mark Abraham. It?s 
really great  tutorial and GROMACS works amazingly fast.
Can someone point me please to the research paper(s)  that describe some 
real life experiments or benchmarks running replica exchange simulations 
with GROMACS? 
I don?t really care if it?s protein folding or something else, but I need 
to be able to easily repeat the experiment/benchmark/etc. by myself and I 
prefer some scenario that takes many hours to run

Can you recommend some relevant research papers?

Thanks
Gil




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Re: [gmx-users] (no subject)

2019-12-08 Thread shakuntala dhurua

here I am using gromacs version --- gromacs-5.1.5

On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar 
wrote:

> Please specify your gromacs version.
>
> On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > hi
> > I am facing problem during hydrogen bond correlation c(t) with error
> > segmentation fault
> > I have used following flag for generate xtc file::- gmx trjconv -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > cluster
> > then for hydrogen bond correlation used following flag ::-gmx hbond -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > following error I am getting
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> > please suggest me to solve this problem
> > --
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Re: [gmx-users] (no subject)

2019-12-08 Thread Tasneem Kausar

Please specify your gromacs version.

On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua 
wrote:

> hi
> I am facing problem during hydrogen bond correlation c(t) with error
> segmentation fault
> I have used following flag for generate xtc file::- gmx trjconv -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> cluster
> then for hydrogen bond correlation used following flag ::-gmx hbond -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> following error I am getting
> Doing autocorrelation according to the theory of Luzar and Chandler.
> Segmentation fault (core dumped)
> please suggest me to solve this problem
> --
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[gmx-users] Queries related to parameterization

2019-12-08 Thread Smruti Sanjita Mishra

Hello Sir/Ma'am

Greetings!

Apologies for the unprecedented message.

I am smruti and being a beginner in gromacs and molecular dynamics field ,
I have some doubts, that I want to clear.

1. My system is just protein , water and some ions. if I am using
charmm27(charmm22 + cmap) and during the solvent model selection, I chose
TIP3P.itp but it did not run, instead it showed error, that tip3p file has
been removed from gromacs/share/top. is it ok to use spc216.gro in the
place of tip3p as they all are three point models.?? and is charmm 27 and
spc216 is the right combination for the system?? and if I want to use tip3p
then how can i proceed with it??

2. In the energy minimization input file(.mdp) if i want to change the
default integrator = steep into ABNR Algorithm then how can i change and
what is the difference basically between two algorithms??

3. In nvt.mdp file, when I changed tcoupl = V-rescale ; modified Berendsen
thermostat into Nose-Hoover it ran upto some steps and then suddenly showed
segmentation error. is it due to the change of default method or any other
reason? and if i want to continue with nose-hoover method then how should i
proceed with it??

waiting for your response :)
Kind Regards,
Smruti Mishra
Bioinformatics Intern - IIIT-H
Dr. Deva Lab (Computational Biology - CCNSB)
Hyderabad - 500032
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[gmx-users] (no subject)

2019-12-08 Thread shakuntala dhurua

hi
I am facing problem during hydrogen bond correlation c(t) with error
segmentation fault
I have used following flag for generate xtc file::- gmx trjconv -n
index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc cluster
then for hydrogen bond correlation used following flag ::-gmx hbond -n
index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
following error I am getting
Doing autocorrelation according to the theory of Luzar and Chandler.
Segmentation fault (core dumped)
please suggest me to solve this problem
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Re: [gmx-users] making movie with VMD

2019-12-08 Thread Dallas Warren

You can get ffmpeg for Windows.

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 Mon, 9 Dec 2019 at 00:34, mmousivand93  wrote:

> Dear all
>
> I performed molecular dynamic simulation(50ns) and I would like to
> prepare movie using VMD, however on Windows, the program VIDEOMACH is
> currently required for all movie generation tasks.I am looking for free
> movie converter packages which can be run on Windows . If you know of
> free movie compression programs that work well on Windows, please  let
> me know
>
> Best regards
>
> Maryam
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Re: [gmx-users] configure gmx with external mpi library - an error

2019-12-08 Thread Gil Vernik

Thank you very much. Using gmx_mpi resolved the issue for me.

Perhaps i missed that part in the documentation  that i need to use 
gmx_mpi.

Thanks again
Gil



From:   Mark Abraham 
To: Discussion list for GROMACS users 
Date:   08/12/2019 15:47
Subject:[EXTERNAL] Re: [gmx-users] configure gmx with external mpi 
library - an error
Sent by:gromacs.org_gmx-users-boun...@maillist.sys.kth.se



Hi,

A build with cmake -DGMX_MPI=on will suffix the installed binaries and
libraries with "_mpi" by default. Gil just needs to use gmx_mpi, not gmx

Mark

On Sun, 8 Dec 2019 at 14:29, Justin Lemkul  wrote:

>
>
> On 12/8/19 8:22 AM, Gil Vernik wrote:
> > I installed open-mpi (mpirun (Open MPI) 4.0.2) on my laptop
> > I then follow instructions
> > 
https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_2019.4_install-2Dguide_index.html-23id1=DwICAg=jf_iaSHvJObTbx-siA1ZOg=-YRCpkqZQamrCezWyJCIug=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg=daJQTfoUDLYkGPJOgf9t9EVUOBDYB0aep-61rOQWycQ=
 
 to install
> > gromacs on my mac.
> > I used
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on
> >
> > I then tried to follow the following tutorial
> >
> 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Tutorials_GROMACS-5FUSA-5FWorkshop-5Fand-5FConference-5F2013_An-5Fintroduction-5Fto-5Freplica-5Fexchange-5Fsimulations-253A-5FMark-5FAbraham-252C-5FSession-5F1B=DwICAg=jf_iaSHvJObTbx-siA1ZOg=-YRCpkqZQamrCezWyJCIug=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg=mFwI4IOAR3jAz1hKA1CiTfU-dBJLqlLtaNjwQI-iKTQ=
 

> >
> > However running mpirun -np 4 gmx mdrun -multidir equil[0123]
> > Results in the following error. Please assist.
> >
> > Thanks a lot
> > Gil
> >
> >
> > mpirun -np 4 gmx mdrun -multidir equil[0123]
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  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. Lemkul   :-) GROMACS - gmx mdrun, 
2019.4
> > (-:
> >
> >  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:
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  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.
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  GROMACS is written by:
> >   Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> > Berendsen
> >

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

2019-12-08 Thread Glenn (Gedaliah) Wolosh

Hi,

Thanks for the response. What is interesting is that the same build on a 
Scientific Linux 7.x environment works fine. It is also hard to explain why the 
other gmx commands work and, so far, only grompp fails. At any rate, I have a 
work around using singularity. I can have gromacs run in a Scientific Linux 7 
container on the Scientific Linux 6.x cluster. I have to finish the testing but 
I got past the grompp segfault.

GW

> On Dec 8, 2019, at 8:35 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> That's clearly a mismatch between the std library headers used at compile
> time and the one used at (dynamic) linking time. I don't know how to fix
> it, but on such systems, I've always resorted to scl environments to get
> the appropriate gcc compiler+libraries, and if so then that would be the
> right time to source the Intel scripts.
> 
> Mark
> 
> On Sun, 8 Dec 2019 at 00:56, Glenn (Gedaliah) Wolosh 
> wrote:
> 
>> Here ya go
>> 
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x2aaab21e63aa in
>> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
>>at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
>> http://tree.cc:98/>
>> 98  ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
>> http://tree.cc/>: No such file or directory.
>>in ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
>> http://tree.cc/>
>> Missing separate debuginfos, use: debuginfo-install
>> glibc-2.12-1.212.el6.x86_64
>> (gdb) bt
>> #0  0x2aaab21e63aa in
>> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
>>at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
>> http://tree.cc:98/>
>> #1  0x2aaab1103c03 in std::_Rb_tree> char const, void (*)(gmx::KeyValueTreeValueBuilder*, gmx
>> ::ISerializer*)>, std::_Select1st> (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)> >, s
>> td::less, std::allocator> void (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)
 
>>> ::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator> char const, void (*)(gmx::KeyValueTreeValueBu
>> ilder*, gmx::ISerializer*)> >, unsigned char const&) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #2  0x2aaab11011f0 in gmx::(anonymous
>> namespace)::ValueSerializer::initSerializers() ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #3  0x2aaab10ffee2 in
>> gmx::serializeKeyValueTree(gmx::KeyValueTreeObject const&,
>> gmx::ISerializer*) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #4  0x2aaab115ca27 in _INTERNAL2c7c030d::do_inputrec(t_fileio*,
>> t_inputrec*, bool, int) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #5  0x2aaab1154df1 in _INTERNAL2c7c030d::do_tpx(t_fileio*, bool,
>> t_inputrec*, t_state*, float (*) [3], float (*) [3], gmx_mtop_t*) () from
>> /afs/cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4
>> 
>> #6  0x2aaab11548ed in write_tpx_state(char const*, t_inputrec const*,
>> t_state const*, gmx_mtop_t const*) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #7  0x2aaab132cae4 in gmx_grompp(int, char**) ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #8  0x2aaab1039549 in gmx::CommandLineModuleManager::run(int, char**)
>> ()
>>   from /afs/
>> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
>> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
>> #9  0x00407928 in main ()
>> 
>> GW

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Re: [gmx-users] configure gmx with external mpi library - an error

2019-12-08 Thread Mark Abraham

Hi,

A build with cmake -DGMX_MPI=on will suffix the installed binaries and
libraries with "_mpi" by default. Gil just needs to use gmx_mpi, not gmx

Mark

On Sun, 8 Dec 2019 at 14:29, Justin Lemkul  wrote:

>
>
> On 12/8/19 8:22 AM, Gil Vernik wrote:
> > I installed open-mpi (mpirun (Open MPI) 4.0.2) on my laptop
> > I then follow instructions
> > http://manual.gromacs.org/2019.4/install-guide/index.html#id1 to install
> > gromacs on my mac.
> > I used
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on
> >
> > I then tried to follow the following tutorial
> >
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
> >
> > However running mpirun -np 4 gmx mdrun -multidir equil[0123]
> > Results in the following error. Please assist.
> >
> > Thanks a lot
> > Gil
> >
> >
> > mpirun -np 4 gmx mdrun -multidir equil[0123]
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  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. Lemkul   :-) GROMACS - gmx mdrun, 2019.4
> > (-:
> >
> >  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:
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  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.
> >:-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> >  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:
> >

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

2019-12-08 Thread Mark Abraham

Hi,

That's clearly a mismatch between the std library headers used at compile
time and the one used at (dynamic) linking time. I don't know how to fix
it, but on such systems, I've always resorted to scl environments to get
the appropriate gcc compiler+libraries, and if so then that would be the
right time to source the Intel scripts.

Mark

On Sun, 8 Dec 2019 at 00:56, Glenn (Gedaliah) Wolosh 
wrote:

> Here ya go
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x2aaab21e63aa in
> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
> at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
> http://tree.cc:98/>
> 98  ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
> http://tree.cc/>: No such file or directory.
> in ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc <
> http://tree.cc/>
> Missing separate debuginfos, use: debuginfo-install
> glibc-2.12-1.212.el6.x86_64
> (gdb) bt
> #0  0x2aaab21e63aa in
> std::local_Rb_tree_decrement(std::_Rb_tree_node_base*) ()
> at ../../../../../gcc-5.4.0/libstdc++-v3/src/c++98/tree.cc:98 <
> http://tree.cc:98/>
> #1  0x2aaab1103c03 in std::_Rb_tree char const, void (*)(gmx::KeyValueTreeValueBuilder*, gmx
> ::ISerializer*)>, std::_Select1st (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)> >, s
> td::less, std::allocator void (*)(gmx::KeyValueTreeValueBuilder*, gmx::ISerializer*)
> > >
> >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator char const, void (*)(gmx::KeyValueTreeValueBu
> ilder*, gmx::ISerializer*)> >, unsigned char const&) ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #2  0x2aaab11011f0 in gmx::(anonymous
> namespace)::ValueSerializer::initSerializers() ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #3  0x2aaab10ffee2 in
> gmx::serializeKeyValueTree(gmx::KeyValueTreeObject const&,
> gmx::ISerializer*) ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #4  0x2aaab115ca27 in _INTERNAL2c7c030d::do_inputrec(t_fileio*,
> t_inputrec*, bool, int) ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #5  0x2aaab1154df1 in _INTERNAL2c7c030d::do_tpx(t_fileio*, bool,
> t_inputrec*, t_state*, float (*) [3], float (*) [3], gmx_mtop_t*) () from
> /afs/cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4
> 
> #6  0x2aaab11548ed in write_tpx_state(char const*, t_inputrec const*,
> t_state const*, gmx_mtop_t const*) ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #7  0x2aaab132cae4 in gmx_grompp(int, char**) ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #8  0x2aaab1039549 in gmx::CommandLineModuleManager::run(int, char**)
> ()
>from /afs/
> cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 <
> http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4>
> #9  0x00407928 in main ()
>
> GW
>
> > On Dec 6, 2019, at 9:39 AM, Mark Abraham 
> wrote:
> >
> > OK, that looks fine.
> >
> > What does the stack trace of the segfault look like? e.g.
> >
> > gdb --args /the/gmx grompp -whatever -args
> >
> > Mark
> >
> > On Fri, 6 Dec 2019 at 15:29, Glenn (Gedaliah) Wolosh  >
> > wrote:
> >
> >>
> >>
> >>> On Dec 6, 2019, at 9:12 AM, Mark Abraham 
> >> wrote:
> >>>
> >>> Hi,
> >>>
> >>> If the environment is sufficiently well constructed to do the necessary
> >>> dynamic linking, then things like gmx -version and gmx editconf should
> >> not
> >>> segfault. Do they? My guess is that the appropriate Intel libraries, or
> >>> perhaps the gcc libstdc++ libraries that icc requires are actually not
> >>> available in the environment.
> >>
> >>
> >> These command do not segfault. The dynamic linking is fine.
> >>
> >> kong-183 lysozyme >: module list
> >> Currently Loaded Modulefiles:
> >>  1) sge3) intel/parallel_studio/2019.4   5)
> >> gromacs/intel/2019.4
> >>  2) singularity/3.2.1  4) gcc/5.4.0
> >>
> >> kong-184 lysozyme >: which gmx
> >> /afs/cad/linux/gromacs/intel/2019.4/bin/gmx
> >> kong-185 lysozyme >: ldd /afs/cad/linux/gromacs/intel/2019.4/bin/gmx
> >>linux-vdso.so.1 =>  (0x7ffd08584000)
> >>libmkl_intel_lp64.so =>
> >>
>

[gmx-users] making movie with VMD

2019-12-08 Thread mmousivand93

Dear all 

I performed molecular dynamic simulation(50ns) and I would like to
prepare movie using VMD, however on Windows, the program VIDEOMACH is
currently required for all movie generation tasks.I am looking for free
movie converter packages which can be run on Windows . If you know of
free movie compression programs that work well on Windows, please  let
me know  

Best regards 

Maryam
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Re: [gmx-users] Chemical reaction

2019-12-08 Thread Justin Lemkul





On 12/8/19 7:12 AM, Sina Omrani wrote:

Hi,
Is it possible to do a simulation with considering probability of chemical
reaction?
I have a simulation box containing CO2 and water and I want to know if
there is a suitable condition that HCO3 could be produced, consider it in
my simulation.


Chemical reactions are quantum mechanical phenomena. You could 
potentially compute reaction pathways from MD snapshots, but again 
that's a QM thing done in different software.


-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] configure gmx with external mpi library - an error

2019-12-08 Thread Justin Lemkul





On 12/8/19 8:22 AM, Gil Vernik wrote:

I installed open-mpi (mpirun (Open MPI) 4.0.2) on my laptop
I then follow instructions
http://manual.gromacs.org/2019.4/install-guide/index.html#id1 to install
gromacs on my mac.
I used
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on

I then tried to follow the following tutorial
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B

However running mpirun -np 4 gmx mdrun -multidir equil[0123]
Results in the following error. Please assist.

Thanks a lot
Gil


mpirun -np 4 gmx mdrun -multidir equil[0123]
   :-) GROMACS - gmx mdrun, 2019.4 (-:

 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. Lemkul   :-) GROMACS - gmx mdrun, 2019.4
(-:

 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:
   :-) GROMACS - gmx mdrun, 2019.4 (-:

 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.
   :-) GROMACS - gmx mdrun, 2019.4 (-:

 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.

Viveca Lindahl

[gmx-users] configure gmx with external mpi library - an error

2019-12-08 Thread Gil Vernik

I installed open-mpi (mpirun (Open MPI) 4.0.2) on my laptop
I then follow instructions 
http://manual.gromacs.org/2019.4/install-guide/index.html#id1 to install 
gromacs on my mac.
I used 
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on

I then tried to follow the following tutorial 
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B

However running mpirun -np 4 gmx mdrun -multidir equil[0123]
Results in the following error. Please assist.

Thanks a lot 
Gil


mpirun -np 4 gmx mdrun -multidir equil[0123]
  :-) GROMACS - gmx mdrun, 2019.4 (-:

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. Lemkul   :-) GROMACS - gmx mdrun, 2019.4 
(-:

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:
  :-) GROMACS - gmx mdrun, 2019.4 (-:

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.
  :-) GROMACS - gmx mdrun, 2019.4 (-:

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.

   Viveca LindahlMagnus Lundborg Erik Marklund

[gmx-users] Chemical reaction

2019-12-08 Thread Sina Omrani

Hi,
Is it possible to do a simulation with considering probability of chemical
reaction?
I have a simulation box containing CO2 and water and I want to know if
there is a suitable condition that HCO3 could be produced, consider it in
my simulation.

Thank you. Regards.
-- 
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Re: [gmx-users] Problem with GROMAC 2019.4

2019-12-08 Thread Paul Buscemi

Are you up And running?

PB

> On Dec 8, 2019, at 12:46 AM, Avi Hundal  wrote:
> 
> Hey Paul,
> 
> Thanks for looking out.  I found that out the hard way, I have gcc 8.0
> installed and configured it with '-config gcc'.
> 
> Regards,
> 
> Avneel S. Hundal
> 
> Email: havn...@gmail.com
> 
> 
>> On Sat, Dec 7, 2019 at 6:39 PM Paul Buscemi  wrote:
>> 
>> A shot in the dark. Cuda may not work with latest version of gcc. There is
>> lit on this issue   Try the repository version for cuda toolbox
>> 
>> PB
>> 
>>> On Dec 4, 2019, at 4:25 AM, Christian Blau  wrote:
>>> 
>>> HI Avneel,
>>> 
>>> 
>>> In general, using the latest stable version is always the first thing to
>> recommend, because this is where your issue might have already been fixed.
>>> 
>>> 
>>> Do you also get the same "unsafe srcdir value" when running make? It'd
>> be interesting to know what system you are using.
>>> 
>>> 
>>> I assume you tried a bunch of things already in the past two weeks, but
>> on the chance that  you did not already you might try:
>>> 
>>>  - try building in a directory with no whitespaces or other special
>> characters in the directory name (usually should not be an issue, but
>> "unsafe srcdir value" hints at this)
>>> 
>>>  - using ninja as a build system (use cmake -GNinja , then type ninja
>> instead of make)
>>> 
>>>  - trying different fft libraries (fftw, mkl, fftpack)
>>> 
>>> 
>>> Also, it'd be great to hear back to know what solved the issue.
>>> 
>>> 
>>> Best,
>>> 
>>> Christian
>>> 
 On 2019-12-04 08:42, Avi Hundal wrote:
 Hi all,
 
 I've been trying to get GROMAC 2019.4 to work on my computer with GPU
 acceleration for over 2 weeks, without success and without trying to
>> bother
 you all here.  Scouring the archives, someone else had the same exact
>> issue
 I have (
 
>> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg33675.html
 ).
 
 The problem occurs after entering "make".  I haven't been able to find a
 solution, and the person who previously had this problem was suggested
>> to
 upgrade to the newest stable version at that time.  Any suggestions?
>> Thank
 you!
 
 Regards,
 
 Avneel S. Hundal
 
 Email: havn...@gmail.com
>>> --
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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[gmx-users] GROMACS for replica exchange - recommendation for the research papers

Re: [gmx-users] (no subject)

Re: [gmx-users] (no subject)

[gmx-users] Queries related to parameterization

[gmx-users] (no subject)

Re: [gmx-users] making movie with VMD

Re: [gmx-users] configure gmx with external mpi library - an error

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Re: [gmx-users] configure gmx with external mpi library - an error

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

[gmx-users] making movie with VMD

Re: [gmx-users] Chemical reaction

Re: [gmx-users] configure gmx with external mpi library - an error

[gmx-users] configure gmx with external mpi library - an error

[gmx-users] Chemical reaction

Re: [gmx-users] Problem with GROMAC 2019.4

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