Understanding what I am installing from VOTCA

75 views
Skip to first unread message

Satyen Dhamankar

unread,
Mar 25, 2021, 10:20:23 PM3/25/21
to votca
Hello,

I am new to coarse-graining and VOTCA, and I want to install VOTCA to run coarse-grained simulation in GROMACS. I use GROMACS 2020.5, and have it on my system.  

I used the following script to get votca on to my system, built for GROMACS, obtained from https://www.votca.org/csg-tutorials/README.html 

prefix=~/votca

version=master # or 'stable' or 'v1.4.1'

git clone -b ${version} --recursive https://github.com/votca/votca.git

cd votca

mkdir build

cd build

cmake -DBUILD_OWN_GROMACS=ON .. 

make -j5 

make install

I collected the stderr and stdout after running this script and attached it to this file. 

My question is, is the software package that I have downloaded meant for GROMACS simulations, and GROMACS simulations only? Would I need to download the non-GROMACS version if I were running simulation using LAMMPS? 

Should I be concerned by the standard output/standard errors that have taken place? there seem to be plenty of things, and I honestly don't know how to process all of the information... 

Thank you for any advice you have!

Satyen

stdoe.txt

Christoph Junghans

unread,
Mar 25, 2021, 10:32:05 PM3/25/21
to vo...@googlegroups.com
On Thu, Mar 25, 2021 at 8:20 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Hello,
>
> I am new to coarse-graining and VOTCA, and I want to install VOTCA to run coarse-grained simulation in GROMACS. I use GROMACS 2020.5, and have it on my system.
Gromacs 2020.5 won't work as it doesn't have support for tabulated
interactions. You build VOTCA with BUILD_OWN_GROMACS=ON below, so it
will download and build gromacs 2019.6 for you.
>
> I used the following script to get votca on to my system, built for GROMACS, obtained from https://www.votca.org/csg-tutorials/README.html
>
> prefix=~/votca
>
> version=master # or 'stable' or 'v1.4.1'
>
> git clone -b ${version} --recursive https://github.com/votca/votca.git
>
> cd votca
>
> mkdir build
>
> cd build
>
> cmake -DBUILD_OWN_GROMACS=ON ..
>
> make -j5
>
> make install
>
> I collected the stderr and stdout after running this script and attached it to this file.
Looking at your output, it seems eigen is missing. CMake warns about
that a couple of times. Also you gcc might be a bit old.

>
> My question is, is the software package that I have downloaded meant for GROMACS simulations, and GROMACS simulations only? Would I need to download the non-GROMACS version if I were running simulation using LAMMPS?
VOTCA will support all MD packages that are on the system. Only
gromacs needs to be there at compile time, the others just need to be
there at runtime.
If you are planning to use LAMMPS you can also build VOTCA without
gromacs support.

>
> Should I be concerned by the standard output/standard errors that have taken place? there seem to be plenty of things, and I honestly don't know how to process all of the information...
Yes, see my comments above.

Christoph

>
> Thank you for any advice you have!
>
> Satyen
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c7de45e4-68de-4f46-ad08-8da9a28377c6n%40googlegroups.com.



--
Christoph Junghans
Web: http://www.compphys.de

Satyen Dhamankar

unread,
Mar 25, 2021, 10:52:13 PM3/25/21
to votca
Thank you so much for your response Christoph! 

when I do gmx -h on my cluster, I still see the following piece in my output: 

GROMACS:      gmx, version 2020.5

Executable:   /home/satyend/.local/bin/gmx

Data prefix:  /home/satyend/.local

Working dir:  /home/satyend

Command line:

  gmx -h 

Does this mean that there is something wrong with my installation of votca? Should I get a fresh copy of Gromacs which is less than 2020.5 (19.6 perhaps)? 

I will get on with updating my gcc version and obtaining Eigen. 

Again, I really appreciate you taking the time to answer my questions!

Christoph Junghans

unread,
Mar 25, 2021, 11:07:43 PM3/25/21
to vo...@googlegroups.com
On Thu, Mar 25, 2021 at 20:52 Satyen Dhamankar <saty...@gmail.com> wrote:
Thank you so much for your response Christoph! 

when I do gmx -h on my cluster, I still see the following piece in my output: 

GROMACS:      gmx, version 2020.5

Executable:   /home/satyend/.local/bin/gmx

Data prefix:  /home/satyend/.local

Working dir:  /home/satyend

Command line:

  gmx -h 

Does this mean that there is something wrong with my installation of votca? Should I get a fresh copy of Gromacs which is less than 2020.5 (19.6 perhaps)? 
If you aren’t planning to use gromacs don’t worry about it, otherwise you will need an older version. Gromacs 2019.* is the last series that supports tabulated potentials.


I will get on with updating my gcc version and obtaining Eigen. 
Alternatively try to use spack to install VOTCA.

Satyen Dhamankar

unread,
Mar 28, 2021, 11:11:28 PM3/28/21
to votca
Hi Christoph, 

Thank you for your advice. I used spack to obtain all of my dependencies using the script: 
git clone clone https://github.com/spack/spack.git spack 
source spack/share/spack/setup-env.sh 
spack install votca-csg

I am going through your tutorials, but I am trying to find the directory where all the executables are so I can run the commands csg_map, csg_dump and so on. At the moment, I am trying to execute the csg_stat and csg_map command (in the atomistic spce simulation), but bash is not finding those commands... 

I really appreciate all of your help! 

Christoph Junghans

unread,
Mar 29, 2021, 10:46:10 AM3/29/21
to vo...@googlegroups.com
On Sun, Mar 28, 2021 at 21:11 Satyen Dhamankar <saty...@gmail.com> wrote:
Hi Christoph, 

Thank you for your advice. I used spack to obtain all of my dependencies using the script: 
git clone clone https://github.com/spack/spack.git spack 
source spack/share/spack/setup-env.sh 
spack install votca-csg

I am going through your tutorials, but I am trying to find the directory where all the executables are so I can run the commands csg_map, csg_dump and so on. At the moment, I am trying to execute the csg_stat and csg_map command (in the atomistic spce simulation), but bash is not finding those commands... 
You can use “spack find -p votca-csg” to see the path.

Also see 
on how to use installed spack packages.

Christoph 
Reply all
Reply to author
Forward
0 new messages