[gmx-users] Clayff in GROMACS

2018-10-23 Thread Nurul Hayati Harolanuar 
Hi,

Is there any possible way where I can get the ClayFF force field directory
files for koalinite for GROMACS?

Thank you in advance.


*NURUL HAYATI BINTI HAROLANUAR*

Bachelor of Engineering (Hons) Petroleum Engineering
Universiti Teknologi PETRONAS
32610 Bandar Seri Iskandar,
Perak Darul Ridzuan,
Malaysia.

(+6)0137686917
hayatiharolan...@gmail.com
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[gmx-users] Fwd: thread_GROMACs_question

2018-10-23 Thread Dallas Warren 
First off, you should keep this on the emailing list.  I have included the
emailing list in the reply.  No need to take it to private email.

Did you read the link that I sent with the reply?  You even have the
simulation box visualised with the vmd screen shot you sent, so that should
be a big clue to you what is going on.  Have a play with the vmd periodic
images tab, it should very quickly make sense.

From what gmx distance says, I don't think you need to use any pbc
processing before doing the calculations, it takes pbc into consideration.
The processing you did has probably messed things up, most likely the
nojump.  And the graphs indicate this fact too.

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, 24 Oct 2018 at 09:32, Antonio Carlesso 
wrote:

> Dear Warren,
>
> I am a PhD student at the University of Göteborg (Sweden).
>
>
> Since you should be an MD expert I would like to ask you one more stuff
> regarding this thread (hope I will not bother you):
>
>
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg34909.html
>
>
>
>
>
>
>
>
>
> Do you have any reason why  calculating the distance over time between
> two pair of atoms (Oxigen of the ligand VS nitrogen of the Lysine in the
> protein) using gmx distance in GROMACs (Figure 1) and VMD(figure 2)  does
> not match ?
>
>
> *Figure1.* Values obtained with gmx distance in GROMACS
>
>
>
>
> *Figure 2.* Value obtained for just one of the previous graph (green one)
> using VMD.
>
>
>
>
>
> for my believe the ligand is actually moving away (picture below).
>
>
>
>
>
> Thank you for your possible help!
>
>
>
> Best regards,
>
> Antonio
>
>
>
>
>
> p.s. to deal with PBC I first make my system “whole” , extract the first
> frame from the trajectory to use as  reference, and then use trjconv -pbc
> nojump with that first frame as reference
>
> aprun -n 1 gmx_mpi trjconv -s md_0_500.tpr -f md_0_500.xtc -o
> md_0_500_whole_dt50.xtc -pbc whole -dt 50
>
>
>
> aprun -n 1 gmx_mpi trjconv -f md_0_500_whole_dt50.xtc  -s md_0_500.tpr -b
> 0 -e 1  -o 1st_frame.gro -pbc mol –center
>
>
>
> aprun -n 1 gmx_mpi trjconv -s 1st_frame.gro -f md_0_500_whole_dt50.xtc -o
> md_0_500_whole_dt50_nojump.xtc -pbc nojump
>
>
>
>
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[gmx-users] Location of latest version of Acpype

2018-10-23 Thread Matthew Fisher 
Dear all,


I'm currently trying to locate the latest version of acpype and have been 
unable to find a working link to the script/installer. Could anyone please 
point me in the right direction?


Thanks,

Matthew Fisher
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Re: [gmx-users] charmm36m version for gromacs

2018-10-23 Thread Carlos Navarro 
Dear Justin,
I'll take a look at the comments.
Thanks for the quick reply.
Best,
Carlos

El mar., 23 oct. 2018 a las 15:17, Justin Lemkul ()
escribió:

>
>
> On 10/23/18 2:15 PM, Carlos Navarro wrote:
> > Dear gromacs users,
> > Where can I download the charmm36m version of charmm for gromacs?
> > I know that here :http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> is
>
> It's CHARMM36m. See the comments at that link that explicitly say what
> is included and how to switch back and forth between C36 and C36m if
> needed.
>
> -Justin
>
> > the  charmm36 version, but since I'm preparing some parts in charmm-gui,
> I
> > want to try the charmm36m version instead.
> > Hope someone can help me.
> > Best regards,
> > Carlos
> > --
> >
> > Carlos Navarro Retamal
> >
> > Bioinformatic Engineering. PhD
> >
> > Postdoctoral Researcher in Center for Bioinformatics and Molecular
> > Simulations
> >
> > Universidad de Talca
> >
> > Av. Lircay S/N, Talca, Chile
> >
> > T: (+56) 712201  798
> >
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
> --
> ==
>
> 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.thelemkullab.com
>
> ==
>
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>


-- 

--

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201  798

E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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Re: [gmx-users] charmm36m version for gromacs

2018-10-23 Thread Justin Lemkul 




On 10/23/18 2:15 PM, Carlos Navarro wrote:

Dear gromacs users,
Where can I download the charmm36m version of charmm for gromacs?
I know that here :http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs is


It's CHARMM36m. See the comments at that link that explicitly say what 
is included and how to switch back and forth between C36 and C36m if needed.


-Justin


the  charmm36 version, but since I'm preparing some parts in charmm-gui, I
want to try the charmm36m version instead.
Hope someone can help me.
Best regards,
Carlos
--

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201  798

E: carlos.navarr...@gmail.com or cnava...@utalca.cl


--
==

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.thelemkullab.com

==

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[gmx-users] charmm36m version for gromacs

2018-10-23 Thread Carlos Navarro 
Dear gromacs users,
Where can I download the charmm36m version of charmm for gromacs?
I know that here :http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs is
the  charmm36 version, but since I'm preparing some parts in charmm-gui, I
want to try the charmm36m version instead.
Hope someone can help me.
Best regards,
Carlos
--

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201  798

E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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[gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

2018-10-23 Thread ABEL Stephane 
Dear all, 

I would like to obtain a 2D density map plot as for instance Fig. 4 in the 
following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein inserted 
in a surfactant micelle with gmx densmap and xpm2ps .  I have few questions 

- Have any of you ever done this type of plot? If yes, how? 
- What parameters for densmap and/or xpm2ps did you use? 
- How did you combine the protein and surfactant xpm files into a single one to 
obtain the same plot as Fig. 4

Thanks in advance for your help 

Stéphane
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[gmx-users] (no subject)

2018-10-23 Thread Ehsan Moravveji 
Dear GMX users,

I would like to share a difficulty installing GROMACS/2018.3 with you. I
use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes
equipped with 4 x P100 Nvidia devices.

Below is the cmake configuration that I use, followed by the error that I
receive. I am not sure if there is still an extra flag to set to resolve
this issue, or some other steps must be taken?

I appreciate your input.

-- 
Kind regards,
Ehsan Moravveji

###
cmake "${cwd}/${dir_src}" \
  -DGMX_SIMD='AVX_512' \
  -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
  -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \
  -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
-DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_INSTALL_PREFIX="${dir_install}" \
  -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
  -DCMAKE_VERBOSE_MAKEFILE=ON \
  -DGMX_MPI=ON \
  -DGMX_GPU=ON \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
  -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
  -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
-DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
  -DCUDA_HOST_COMPILER="${PATH_NVCC}"
-DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
  -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
  -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
-DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
  -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
  -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
  -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
-DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \

-DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
\
  -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF

###

-- Generating dependency file:
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
/apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/
nbnxn_cuda.cu -o
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
-ccbin /apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -m64 --std
c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H
-DUSE_STD_INTTYPES_H -Xcompiler
,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\"
-gencode arch=compute_60,code=sm_60 -gencode
arch=compute_60,code=compute_60 -use_fast_math -gencode
arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC
-I/apps/leuven/skylake/2018a/software/CUDA/9.2.148/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/lmfit
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src
-I/apps/leuven/skylake/2018a/software/hwloc/1.11.11-GCCcore-6.4.0/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/tng_io/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/tng/include
nvcc fatal   : 'avx512f': expected a number
CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219
(message):
  Error generating

/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o
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Re: [gmx-users] gmx kill computer?

2018-10-23 Thread Wahab Mirco 
On 23.10.2018 15:12, Michael Brunsteiner wrote:
> the computers are NOT overclocked, cooling works, cpu temperatures are well 
> below max.
> as stated above something like this happened three times, each time with gmx 
> at full blastand with the same type of nvidia card ... can it be that my 
> hardware has some issue that isso well hidden that only gromacs running at 
> full blast can trigger it? - has anybody observedsuch behaviour before, or 
> suggestions on how to better diagnose the issue ... ??
> 
> the specs:
> workstation 1Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz + nvidia geforce gtx 
> 1060
> running debian stretch with nvidia driver version 387.26
> workstation 2AMD Ryzen 7 2700X Eight-Core Processor + nvidia geforce gtx 1060
> running debian stretch with  nvidia driver version 390.87

GTX-1060, due to the interval-like offloading of gpu-related work will
possibly generate some really nasty load-changes the power supply can't
cope with. It is well known that fast load changes of modern graphics
cards may overstrain the power supply unit if not "strong" enough.

The symptoms very much suggest a problem with the PSU. Maybe
Szilard Páll can comment on this.


Regards

M.
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Re: [gmx-users] gmx kill computer?

2018-10-23 Thread Harry Mark Greenblatt 
BS”D

I had a similar issue with a workstation, and it turned out to be the power 
supply, which is why it seemed that someone pulled the plug (at least it seems 
to be the PSU, since having replaced it we don’t see failures).  The problem 
was very intermittent, and did not require any great load.  The system never 
had time to write any kind of error to the disk.  *But* our supplier said that 
there can be other problems that give rise to this sudden death.

If you can, see if swapping the power supply helps.

Harry



On 23 Oct 2018, at 4:11 PM, Michael Brunsteiner 
mailto:mbx0...@yahoo.com>> wrote:


Hi,
this might be considered off-topic, but i believe there is some evidence to the 
contrary ... what i see is this:
I have a couple of (fairly new) workstations (specs below) and on at least two 
of them, on at least three differentoccasions, i recently saw the following 
behaviour:computer is happily running and all of sudden stops doing so, as if 
somebody had pulled the plug.I need to turn it back on manually (i.e. it didn't 
just hang, or reboot - it actually turned itself off)the ONLY common factor I 
see is that in each of the three cases the computer, at the time when it 
died,had a gromacs job running with both CPU and GPU (with the same type of 
card) at full load ... (the samecomputers running cp2k or orca which are also 
quite heavy on the CPU, but not the GPU never showed issues)

e.g.:
in /var/log/syslog there's just a normal log for a cron-job, at 12:03,then at 
12:10 an edr file from a running gmx job is written to the last timethen a few 
minutes later the computer dies without further notice.
the next /var/log/syslog entry is from 12:31 when i turned the computer on 
again and it starts booting.there is also NOTHING conspicuous in any of the 
other files in /var/log, or in any ofthe output files or stdout/stderr from the 
running gmx job.
the computers are NOT overclocked, cooling works, cpu temperatures are well 
below max.
as stated above something like this happened three times, each time with gmx at 
full blastand with the same type of nvidia card ... can it be that my hardware 
has some issue that isso well hidden that only gromacs running at full blast 
can trigger it? - has anybody observedsuch behaviour before, or suggestions on 
how to better diagnose the issue ... ??

I'd be grateful for any help!
thanks, michael

the specs:
workstation 1Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz + nvidia geforce gtx 1060
running debian stretch with nvidia driver version 387.26
workstation 2AMD Ryzen 7 2700X Eight-Core Processor + nvidia geforce gtx 1060
running debian stretch with  nvidia driver version 390.87




=== Why be happy when you could be normal?
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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

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[gmx-users] gmx kill computer?

2018-10-23 Thread Michael Brunsteiner 

Hi,
this might be considered off-topic, but i believe there is some evidence to the 
contrary ... what i see is this:
I have a couple of (fairly new) workstations (specs below) and on at least two 
of them, on at least three differentoccasions, i recently saw the following 
behaviour:computer is happily running and all of sudden stops doing so, as if 
somebody had pulled the plug.I need to turn it back on manually (i.e. it didn't 
just hang, or reboot - it actually turned itself off)the ONLY common factor I 
see is that in each of the three cases the computer, at the time when it 
died,had a gromacs job running with both CPU and GPU (with the same type of 
card) at full load ... (the samecomputers running cp2k or orca which are also 
quite heavy on the CPU, but not the GPU never showed issues) 

e.g.: 
in /var/log/syslog there's just a normal log for a cron-job, at 12:03,then at 
12:10 an edr file from a running gmx job is written to the last timethen a few 
minutes later the computer dies without further notice.
the next /var/log/syslog entry is from 12:31 when i turned the computer on 
again and it starts booting.there is also NOTHING conspicuous in any of the 
other files in /var/log, or in any ofthe output files or stdout/stderr from the 
running gmx job.
the computers are NOT overclocked, cooling works, cpu temperatures are well 
below max.
as stated above something like this happened three times, each time with gmx at 
full blastand with the same type of nvidia card ... can it be that my hardware 
has some issue that isso well hidden that only gromacs running at full blast 
can trigger it? - has anybody observedsuch behaviour before, or suggestions on 
how to better diagnose the issue ... ??

I'd be grateful for any help!
thanks, michael

the specs:
workstation 1Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz + nvidia geforce gtx 1060
running debian stretch with nvidia driver version 387.26
workstation 2AMD Ryzen 7 2700X Eight-Core Processor + nvidia geforce gtx 1060
running debian stretch with  nvidia driver version 390.87  




=== Why be happy when you could be normal?
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Re: [gmx-users] Turn on/off residues in gromacs

2018-10-23 Thread Justin Lemkul 




On 10/23/18 8:08 AM, Quyen Vu Van wrote:

Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?


I understand exactly what you're trying to do and my comments are a 
direct response to that. This is not a reasonable model for what you 
want to study, for the reasons stated below.


-Justin


Best regards,
Quyen

On Mon, Oct 22, 2018, 14:11 Justin Lemkul  wrote:



On 10/22/18 7:29 AM, Quyen Vu Van wrote:

Dear all,
sorry for my unclear question,
I attached here the quick draw picture of what I am saying, please take a
look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0

What you are trying to do is both technically challenging and physically
questionable. The free energy options allow you to modulate the
interactions of a [moleculetype] with the remainder of the system; you
can't easily decompose individual residues of a protein, which is part
of a single [moleculetype]. You could manually define A- and B- states
in the topology and there are various tools to do that.

The bigger problem is, even if you accomplish what you seek in terms of
the technical setup, it's physically unrealistic. As Mark noted, you
have an unsatisfied valence at the C-terminus of each residue at each
interval of time. This is not physically real, as amino acids are simply
transferred between tRNA and onto the growing polypeptide chain. Simply
"growing" residues onto the chain will not come close to mimicking
protein synthesis in any meaningful way.

-Justin


Thank you and best regards,
Quyen

On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van 

wrote:

Dear Mark,
I mean that e.g my protein has 10 residues in pdb file but at t=0,

Gromacs

will only calculate the interactions of all atoms in residue 1
t= 1ns (for example) Gromacs will calculate the interactions of all

atoms

in residues 1 and 2, and so on till t= XXX ns, interactions of all

atoms of

full protein is take into account.
Best regards,
Quyen


On Fri, Oct 19, 2018, 18:42 Mark Abraham 

wrote:

Hi,

What do you mean by turning a residue off? What would terminate the
chemical bond to the residue that it was bound to?

Mark

On Fri, Oct 19, 2018, 14:40 Quyen Vu Van  wrote:


Dear Gromacs community,
How can I turn off/on residues in the protein, I want to mimic the

process

of protein synthesis.
Thank you and best regards,
Quyen
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Virginia Tech Department of Biochemistry

303 Engel Hall
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Virginia Tech Department of Biochemistry

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

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http://www.thelemkullab.com

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Re: [gmx-users] Turn on/off residues in gromacs

2018-10-23 Thread Quyen Vu Van 
Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?
Best regards,
Quyen

On Mon, Oct 22, 2018, 14:11 Justin Lemkul  wrote:

>
>
> On 10/22/18 7:29 AM, Quyen Vu Van wrote:
> > Dear all,
> > sorry for my unclear question,
> > I attached here the quick draw picture of what I am saying, please take a
> > look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0
>
> What you are trying to do is both technically challenging and physically
> questionable. The free energy options allow you to modulate the
> interactions of a [moleculetype] with the remainder of the system; you
> can't easily decompose individual residues of a protein, which is part
> of a single [moleculetype]. You could manually define A- and B- states
> in the topology and there are various tools to do that.
>
> The bigger problem is, even if you accomplish what you seek in terms of
> the technical setup, it's physically unrealistic. As Mark noted, you
> have an unsatisfied valence at the C-terminus of each residue at each
> interval of time. This is not physically real, as amino acids are simply
> transferred between tRNA and onto the growing polypeptide chain. Simply
> "growing" residues onto the chain will not come close to mimicking
> protein synthesis in any meaningful way.
>
> -Justin
>
> > Thank you and best regards,
> > Quyen
> >
> > On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van 
> wrote:
> >
> >> Dear Mark,
> >> I mean that e.g my protein has 10 residues in pdb file but at t=0,
> Gromacs
> >> will only calculate the interactions of all atoms in residue 1
> >> t= 1ns (for example) Gromacs will calculate the interactions of all
> atoms
> >> in residues 1 and 2, and so on till t= XXX ns, interactions of all
> atoms of
> >> full protein is take into account.
> >> Best regards,
> >> Quyen
> >>
> >>
> >> On Fri, Oct 19, 2018, 18:42 Mark Abraham 
> wrote:
> >>
> >>> Hi,
> >>>
> >>> What do you mean by turning a residue off? What would terminate the
> >>> chemical bond to the residue that it was bound to?
> >>>
> >>> Mark
> >>>
> >>> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van  wrote:
> >>>
>  Dear Gromacs community,
>  How can I turn off/on residues in the protein, I want to mimic the
> >>> process
>  of protein synthesis.
>  Thank you and best regards,
>  Quyen
>  --
>  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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> 
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
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> >>> posting!
> >>>
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> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
>
> --
> ==
>
> 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.thelemkullab.com
>
> ==
>
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Re: [gmx-users] phosphorylated residues simulation usinh gromacs

2018-10-23 Thread Benson Muite 
Hi,

Following may be helpful:

http://manual.gromacs.org/documentation/2019-beta1/user-guide/force-fields.html#gmx-amber-ff

Regards,

Benson

On 10/23/18 11:52 AM, farial tavakoli wrote:
> Dear GMX users
> I need to simulate the complex composed of a protein and a peptide which has 
> phosphotyrosine using AMBER99SB force field in GROMACS. cited to the " 
> https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/index.html " 
> to download .OFF and .FRCMOD files of phosphotyrosine. but now I dont know 
> how to use these files in GROMACS. There is no AMBER tutorial in gromacs . I 
> searched google to find that but couldnt find stage by stage guides. Is there 
> anyone can help me how I should use these files in GROMACS?I am sorry because 
> of my english.
> Thanks in advanceFarial

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[gmx-users] phosphorylated residues simulation usinh gromacs

2018-10-23 Thread farial tavakoli 
Dear GMX users
I need to simulate the complex composed of a protein and a peptide which has 
phosphotyrosine using AMBER99SB force field in GROMACS. cited to the " 
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/index.html " 
to download .OFF and .FRCMOD files of phosphotyrosine. but now I dont know how 
to use these files in GROMACS. There is no AMBER tutorial in gromacs . I 
searched google to find that but couldnt find stage by stage guides. Is there 
anyone can help me how I should use these files in GROMACS?I am sorry because 
of my english.
Thanks in advanceFarial
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Re: [gmx-users] Specifying more than one index group via the command line

2018-10-23 Thread Francisco Lobo Cabrera 
Yes thank you I thought it had to be specified with a specific command in
GROMACS.
In effect, just linux works.

Francisco

On Tue, Oct 23, 2018 at 10:15 AM Peter Stern 
wrote:

> Hi,
>
> This is really a linux and not a gromacs question.  There are many ways of
> inputting data to a script depending upon which shell you use.
> One way is to input the data from a file.
> You should google how to do this for the shell you use (bash, tcsh, etc.)
> and choose the solution which suits you.
>
> Peter
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Francisco
> Lobo Cabrera
> Sent: Tuesday, October 23, 2018 10:24 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Specifying more than one index group via the command
> line
>
> Hello:
>
> Is it possible to specify several index groups through the command line?
>
> For example, to compute hydrogen bonds, hbond needs two index groups. This
> can be done through the interactive prompt, but I need to submit this
> instruction wtih a script. I have searched around but have not found
> anything.
>
> Thank you for your attention.
>
> Francisco
> --
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Re: [gmx-users] Specifying more than one index group via the command line

2018-10-23 Thread Francisco Lobo Cabrera 
Thank you, that worked.

Francisco

On Tue, Oct 23, 2018 at 10:14 AM Mark Abraham 
wrote:

> Hi,
>
> See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Mark
>
> On Tue, Oct 23, 2018, 09:28 Francisco Lobo Cabrera <
> francisco.lo...@gmail.com> wrote:
>
> > Hello:
> >
> > Is it possible to specify several index groups through the command line?
> >
> > For example, to compute hydrogen bonds, hbond needs two index groups.
> This
> > can be done through the interactive prompt, but I need to submit this
> > instruction wtih a script. I have searched around but have not found
> > anything.
> >
> > Thank you for your attention.
> >
> > Francisco
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> >
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Re: [gmx-users] Specifying more than one index group via the command line

2018-10-23 Thread Peter Stern 
Hi,

This is really a linux and not a gromacs question.  There are many ways of 
inputting data to a script depending upon which shell you use.
One way is to input the data from a file.  
You should google how to do this for the shell you use (bash, tcsh, etc.) and 
choose the solution which suits you.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Francisco Lobo 
Cabrera
Sent: Tuesday, October 23, 2018 10:24 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Specifying more than one index group via the command line

Hello:

Is it possible to specify several index groups through the command line?

For example, to compute hydrogen bonds, hbond needs two index groups. This can 
be done through the interactive prompt, but I need to submit this instruction 
wtih a script. I have searched around but have not found anything.

Thank you for your attention.

Francisco
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Re: [gmx-users] Specifying more than one index group via the command line

2018-10-23 Thread Mark Abraham 
Hi,

See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

Mark

On Tue, Oct 23, 2018, 09:28 Francisco Lobo Cabrera <
francisco.lo...@gmail.com> wrote:

> Hello:
>
> Is it possible to specify several index groups through the command line?
>
> For example, to compute hydrogen bonds, hbond needs two index groups. This
> can be done through the interactive prompt, but I need to submit this
> instruction wtih a script. I have searched around but have not found
> anything.
>
> Thank you for your attention.
>
> Francisco
> --
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[gmx-users] Specifying more than one index group via the command line

2018-10-23 Thread Francisco Lobo Cabrera 
Hello:

Is it possible to specify several index groups through the command line?

For example, to compute hydrogen bonds, hbond needs two index groups. This
can be done through the interactive prompt, but I need to submit this
instruction wtih a script. I have searched around but have not found
anything.

Thank you for your attention.

Francisco
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