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List of Books (Comp. Biophysics Group)

A.B. Pippard - The Elements of Classical Thermodynamics
Andrew R. Leach - Molecular Modelling: Principles and Applications
Arfken, Weber, Harris - Mathematical Methods for Physicists
Attila Szabo - Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory
Ben Lambert - A Student’s Guide to Bayesian Statistics
Biman Bagchi - Statistical Mechanics for Chemistry and Material Science
David Chandler - Introduction to Modern Statistical Mechanics
David J. Griffiths - Introduction to Electrodynamics
David M. Bishop - Group Theory and Chemistry
D.N. Sathyanarayana - Handbook of Molecular Spectroscopy
Edward M. Purcell - Electricity and Magnetism
E. Balaguruswamy - Object-Oriented Programming with C++
E.T. Jaynes - Probability Theory: The Logic of Science
Feynman, Leighton, and Sands - The Feynman Lectures on Physics - Volume I, II, and III
F. Reif - Statistical Physics
George F. Simmons - Differential Equations with Applications and Historical Notes
Goldstein - Classical Mechanics
Greiner, Neise, Stocker - Thermodynamics and Statistical Mechanics
Herman J.C. Berendsen - A Student’s Guide to Data and Error Analysis
Ilya Prigogine - Non-equilibrium Statistical Mechanics
Jacob Millman, Christos C. Halkias - Integrated Electronics
James P. Sethna - Statistical Mechanics: Entropy, Order Parameters, and Complexity
John David Jackson - Classical Electrodynamics (An Indian Adaptation)
Ken A. Dill, Sarina Bromberg - Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience
Kerson Huang - Statistical Mechanics
Kurt Binder, Dieter W. Heermann - Monte Carlo Simulation in Statistical Physics
Landau and Lifshitz - Theory of Elasticity
Mark W. Zemansky, Richard H. Dittman - Heat and Thermodynamics
Mehran Kardar - Statistical Physics of Particles
Michael P. Allen, Dominic J. Tildesley - Computer Simulation of Liquids
Palash B. Pal - An Introductory Course of Statistical Mechanics
Paul C. Hiemenz - Polymer Chemistry (The Basic Concepts)
Philip R. Benington, D. Keith Robinson - Data Reduction and Error Analysis for the Physical Sciences
R.K. Pathria - Statistical Mechanics
R. Shankar - Principles of Quantum Mechanics
Steven C. Chapra, Raymond P. Canale - Numerical Methods for Engineers
Terrell L. Hill - Statistical Mechanics: Principles and Selected Applications
V. Rajaraman - Computer Programming in Fortran 90 and 95

Installation Guide for GROMACS, PLUMED etc.

Installing GROMACS 2018 with PLUMED:

1. Installing PLUMED

To install PLUMED, use the following commands:

./configure --prefix="/home/mb/softies/plumed235" --enable-mpi --disable-almost --enable-matheval CXX=mpiCC
make -j 8 && make install

Note: PLUMED and GROMACS should use the same MPI libraries.

2. Configuring GROMACS with PLUMED

Navigate to the GROMACS source directory:

cd /path/to/gromacs/source
export PLUMED_ROOT="/home/mb/softies/src/plumed-2.5.1"

In your ~/.bash_aliases file, add:

source ~/softies/src/plumed-2.5.1/sourceme.sh

Then, apply the changes:

source ~/.bash_aliases

Patch GROMACS with PLUMED:

/home/mb/softies/src/plumed-2.5.1/src/lib//plumed patch -p

Create a build directory and compile GROMACS:

mkdir build && cd build/
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/home/mb/softies/gro2018_cuda -DGMX_GPU=CUDA -DGMX_MPI=OFF -DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DCMAKE_CXX_COMPILER=/usr/bin/g++-8

Remove duplicate references to Plumed.o from:

build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt

Finally, compile and install GROMACS:

make -j 8 && make install

Alternative Compilation (Used Previously)

cmake -DGMX_MPI=ON .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/home/fr/fr_fr/fr_mb1148/progs/gro506_alt -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_THREAD_MPI=OFF

PARAM-Shakti Setup

1. Installing FFTW

module load compiler/openmpi/4.0.2
./configure --enable-float --enable-threads --enable-openmp --enable-mpi --enable-shared MPICC=mpicc --prefix=/home/mbiswas.nitr/programs/fftw3 --enable-sse2 --enable-avx --enable-avx2

Loaded Modules

compiler/openmpi/4.0.2
compiler/gcc/8.3.0
lib/fftw3/3.3.8/intel2018
mpich/3.3.1
compiler/cuda/10.2
compiler/cmake/3.15.4

2. Installing GROMACS 2018

cmake .. -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=OFF -DCMAKE_PREFIX_PATH=/home/mbiswas.nitr/programs/fftw3 -DCMAKE_INSTALL_PREFIX=/home/mbiswas.nitr/programs/gro2018_mpi_cuda -DGMX_MPI=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DBUILD_SHARED_LIBS=off

PLUMED with MATHEVAL

1. Setting Up libmatheval

Follow the procedure described in Davide’s message to create a libmatheval distribution without Guile:

🔗 Google Groups: libmatheval Setup

Set the library path so that PLUMED finds libmatheval.so.1:

export LD_LIBRARY_PATH=/PATH_TO/libmatheval/lib/:$LD_LIBRARY_PATH

2. Configuring PLUMED with libmatheval

Modify Makefile.conf:

DYNAMIC_LIBS=-lstdc++ -llapack -lblas -lmatheval -L/PATH_TO_MATHEVAL_LIB
CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) -D__PLUMED_HAS_MATHEVAL -I/lustre/jhome19/esmi19/esmi1901/Programs/libmatheval/lib
LDFLAGS=-rdynamic -L/lustre/jhome19/esmi19/esmi1901/Programs/libmatheval/lib/.libs

Compile PLUMED with libmatheval:

./configure --prefix=/home/fr/fr_fr/fr_mb1148/progs/plumed221 --enable-mpi CXX=mpiCC LDFLAGS=-L/home/fr/fr_fr/fr_mb1148/progs/matheval/lib CPPFLAGS=-I/home/fr/fr_fr/fr_mb1148/progs/matheval/include

GROMACS-2024.5 with PLUMED-2.9.3 Installation on KALAM

Extract the compressed files for PLUMED and GROMACS.

tar -xvzf plumed-2.9.3.tgz
tar -xvzf gromacs-2024.5.tar.gz

PLUMED Installation:

cd /path/to/plumed-2.9.3
./configure --prefix="/home/mb/softies/plumed293" --enable-mpi --disable-almost --enable-matheval CXX=mpiCC

make -j 32 && make install

GROMACS Installation:

export PLUMED_ROOT="/home/mb/softies/src/plumed-2.9.3"
source $PLUMED_ROOT/sourceme.sh
cd /path/to/gromacs-2024.5
$PLUMED_ROOT/src/lib/plumed patch -p

Patch the nearest recent version for the GROMACS Installation.

mkdir build && cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=/home/mb/softies/gro2024_cuda_plumed_mpi -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/usr/bin/gcc-12 -DCMAKE_CXX_COMPILER=/usr/bin/g++-12
make -j 32 && make install

Check whether GROMACS and PLUMED are compiled with OpenMP:

ldd ~/softies/plumed293/bin/plumed
ldd ~/softies/gro2024_cuda_plumed_mpi/bin/gmx_mpi

If you see libraries like, libgomp.so.1 or libmpich.so.12, then they were compiled with MPI indeed.

References

MPI Rank ERROR on KALAM:

If the mpirun and mpiexec are compiled with MPICH Library, it will require more than one node to run. If the system doesn't have that many nodes it will fail. So, in that case, using OpenMP library is recommended.

So, to check which library the mpirun and mpiexec are using,

update-alternatives --get-selections | grep mpi

If you see the following output linked with mpich, then Linking to OpenMP is the best Practice.

mpi auto /usr/bin/mpicc.mpich
mpirun auto /usr/bin/mpirun.mpich
mpi-x86_64-linux-gnu auto /usr/include/x86_64-linux-gnu/mpich

Reinstall the OpenMPI bin and Library.

sudo apt-get install --reinstall openmpi-bin

Then Check again,

$> update-alternatives --get-selections | grep mpi

mpi auto /usr/bin/mpicc.openmpi
mpirun auto /usr/bin/mpirun.openmpi
mpi-x86_64-linux-gnu auto /usr/include/x86_64-linux-gnu/mpich

Now one can use mpirun or mpiexec to use GROMACS with PLUMED.

mpiexec -np 2 --oversubscribe gmx_mpi mdrun -plumed plumed.dat

NAMD

NAMD MPI Notes:

MPI Executable

Build Date: 03/03/10
Compiler: Intel (10.1.015)
Libraries:
- FFTW (2.1.5)
- MVAPICH (0.9.9)
- Charm++ (6.1.3)
Location: /apps/namd/2.7b2/Linux-x86_64-MPI-icc

Notes

To build Charm++, use:
./build charm++ mpi-linux-amd64

For NAMD configuration, run:
./config Linux-x86_64-MPI-icc --charm-arch mpi-linux-amd64

A custom architecture file was created:
arch/Linux-x86_64-MPI-icc.arch (contents below)

MPI Environment Requirement:
To run this executable, your MPI environment must be set by loading the intel/10.1 and mvapich/0.9.9 modules.

Custom Architecture File

Architecture Settings:
NAMD_ARCH = Linux-x86_64
CHARMARCH = mpi-linux-amd64

Compiler Settings:

CXX = mpiCC
FLOATOPTS = -axW -ip -fno-rtti
CXXOPTS = -i-static -static-libgcc -O2 $(FLOATOPTS)
CXXNOALIASOPTS = -O3 -fno-alias $(FLOATOPTS)

CC = mpicc
COPTS = -i-static -static-libgcc -O2 $(FLOATOPTS)

Modifications in FFTW Configuration

The Linux-x86_64.fftw file was modified to:

FFTDIR=/opt/lib/fftw/2.1.5
FFTINCL=-I$(FFTDIR)/include
FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
FFTFLAGS=-DNAMD_FFTW
FFT=$(FFTINCL) $(FFTFLAGS)

Modifications in TCL Configuration

The Linux-x86_64.tcl file was modified to:

TCLDIR=/usr
TCLINCL=-I$(TCLDIR)/include
TCLLIB=-L$(TCLDIR)/lib64 -ltcl8.4 -ldl
TCLFLAGS=-DNAMD_TCL
TCL=$(TCLINCL) $(TCLFLAGS)

GROMACS output selected frames from trajectory

#!/bin/bash # USAGE: trjconv -f metadyn.trr -s metadyn.tpr -o frames/frame.gro -sep -e 4 -exec "./execonframes.sh" #current_frame=`echo ${1:1}` current_frame=`echo ${1}`frames=`awk '{print $1}' ../analysis/projMeta_sphihb_ondPCA.s1000.b50.m100.frames`#echo $frames#echo $current_frame[[ $frames =~ (^|[[:space:]])"$current_frame"($|[[:space:]]) ]] || rm frames/frame${current_frame}.gro

GROMACS replica runs with GPUs

#!/bin/bash # USAGE: trjconv -f metadyn.trr -s metadyn.tpr -o frames/frame.gro -sep -e 4 -exec "./execonframes.sh"#current_frame=`echo ${1:1}`current_frame=`echo ${1} frames=`awk '{print $1}' ../analysis/projMeta_sphihb_ondPCA.s1000.b50.m100.frames`\#echo $frames#echo $current_frame[[ $frames =~ (^|[[:space:]])"$current_frame"($|[[:space:]]) ]] || rm frames/frame${current_frame}.gro

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-February/118715.html

https://sites.google.com/site/drammhto/methods-codes/1-method-of-replica-exchange-with-gromacs

GIT README

#create/clonegit init, git clone ssh://user@server/PATH_TO_DIRECTORY/.git
#add/filesgit add FILE.tex #commit new files/changesgit commit -m "Start with an outline"
#statusgit status
#existing branchesgit branch [-a]#new branchgit branch mithun
#change to branchgit checkout mithun HELP: 1. http://boopsboops.blogspot.de/2013/08/writing-scientific-papers-with-git-and.html

LATEX

LATEX figure merge with tabular:\documentclass[a4paper,12pt]{article}\usepackage{graphicx}\usepackage{subcaption}

\begin{document}

\begin{figure}[htb]\centering \begin{tabular}{@{}cccc@{}} \includegraphics[width=.23\textwidth]{example-image-a} & \includegraphics[width=.23\textwidth]{example-image-b} & \includegraphics[width=.23\textwidth]{example-image-c} & \includegraphics[width=.23\textwidth]{example-image} \\ \includegraphics[width=.23\textwidth]{example-image-a} & \includegraphics[width=.23\textwidth]{example-image-b} & \includegraphics[width=.23\textwidth]{example-image-c} & \includegraphics[width=.23\textwidth]{example-image} \\ \includegraphics[width=.23\textwidth]{example-image-a} & \includegraphics[width=.23\textwidth]{example-image-b} & \includegraphics[width=.23\textwidth]{example-image-c} & \includegraphics[width=.23\textwidth]{example-image} \\ \multicolumn{4}{c}{\includegraphics[width=.23\textwidth]{example-image-a}} \end{tabular} \caption{This is some figure side by side}\end{figure}\end{document}
with subfigure:\documentclass[a4paper,12pt]{article}\usepackage{graphicx}\usepackage{subcaption}
\begin{document}\begin{figure}[htb]\centering \begin{subfigure}[b]{.24\linewidth} \centering \includegraphics[width=.99\textwidth]{example-image-a} \caption{A subfigure}\label{fig:1a} \end{subfigure}% \begin{subfigure}[b]{.24\linewidth} \centering \includegraphics[width=.99\textwidth]{example-image-b} \caption{A subfigure}\label{fig:1b} \end{subfigure}% \caption{This is lot of figures arranged side by side in matrix form with captions for each and a main caption}\label{fig:1}\end{figure}\end{document}
Link: http://tex.stackexchange.com/questions/84889/combining-multiple-eps-files-into-a-single-figure

GNUPLOT

gnuplot colormaps:

http://ayapin-film.sakura.ne.jp/Gnuplot/Primer/Misc/colormap.html

http://jswails.wikidot.com/gnuplot-color-schemes

gnuplot ternary operator

http://gnuplot.sourceforge.net/docs_4.2/node133.html

http://www.phyast.pitt.edu/~zov1/gnuplot/html/statistics.html

gnuplot contour :

set parametric

set contour base

set view 0,0,1

unset surface

set cntrparam levels 5

splot’results.dat’ using 1:2:3 with line

Some tricks with gnuplot:

http://gnuplot-tricks.blogspot.de

Gnuplot 'every' keyword:

every I:J:K:L:M:N

I : Line increment

J : Data block increment

K : The first line

L : The first data block

M : The last line

N : The last data block

every 2 : plot every 2 line

every ::3 : plot from the 3-rd lines

every ::3::5 : plot from the 3-rd to 5-th lines

every ::0::0 : plot the first line only

every 2::::6 : plot the 1,3,5,7-th lines

every :2 : plot every 2 data block

every :::5::8 : plot from 5-th to 8-th data blocks

RAMACOLOR PLOTS

ramacolor --store stores average color for each residue for given state

for i in {1..71}; do ramacolor -d inner_5_8M.dih -s inner_5_8M.dih.cossin.clust/microstates --store ramastore/${i}.rc $i;done [can be parallelized]

ramacolor --load {1..30}.rc --export ramacolor_md.pdf

OLANGEVIN INSTALL

git clone mb1148@bmdlogin.physik.uni-freiburg.de:/u3/langevin/src/olangevin olangevin

git branch working_b1 origin/working_b1

git checkout working_b1

make clean

make

make install

git commit -a -m "compiled b1"

BOOST

Boost install script

#!/bin/bash

GCC_LOC="/home/biswasm/programs/gcc730/bin"

#export AR="${GCC_LOC}/ar"

export CC="${GCC_LOC}/gcc_730"

export CPP="${GCC_LOC}/gcc_730 -E"

export CXX="${GCC_LOC}/g++_730"

export CXXCPP="${GCC_LOC}/g++_730 -E"

pushd boost_${BOOST_DL_VERSION} > /dev/null

# add our compiler to the end of the boost jam config file

echo "using gcc : 7.3 : ${GCC_LOC}/g++_730 ; " >> ./tools/build/src/user-config.jam

#BOOST_LIBRARIES=filesystem,python,regex,system

#CONFIGURE_OPTIONS="--with-python-version=2.7 --with-python-root=${PYTHON_LOC}/${OS}/${ARCH} --with-python=${PYTHON_LOC}/${OS}/${ARCH}/bin/python"

PREFIX="/home/biswasm/programs/boost168"

./bootstrap.sh --prefix=${PREFIX} #--with-libraries=${BOOST_LIBRARIES} ${CONFIGURE_OPTIONS}

./b2 $CPPFLAGS --toolset=gcc

cmake with boost:

#!/bin/bash

BUILDDIR="/home/biswasm/programs/src/Clustering/build"

PREFIXDIR="/home/biswasm/programs/clustering"

GCC_LOC="/home/biswasm/programs/gcc730/bin"

export CC="${GCC_LOC}/gcc_730"

export CXX="${GCC_LOC}/g++_730"

export BOOST_ROOT="/home/biswasm/programs/boost168"

export BOOST_INCLUDE="/home/biswasm/programs/boost168/include"

export BOOST_LIBDIR="/home/biswasm/programs/boost168/lib"

export BOOST_OPTS="-DBOOST_ROOT=${BOOST_ROOT} -DBOOST_INCLUDEDIR=${BOOST_INCLUDE} -DBOOST_LIBRARYDIR=${BOOST_LIBDIR} -DCMAKE_INSTALL_PREFIX=${PREFIXDIR}"

# -DCMAKE_C_COMPILER=gcc_730 -DCMAKE_CXX_COMPILER=g++_730"

(cd ${BUILDDIR} && cmake .. ${BOOST_OPTS} -DCMAKE_C_COMPILER=/home/biswasm/programs/gcc730/bin/gcc_730 -DCMAKE_CXX_COMPILER=/home/biswasm/programs/gcc730/bin/g++_730)

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/biswasm/programs/gcc730/lib64:/home/biswasm/programs/boost168/lib

SLURM JOB SUBMISSION SCRIPT

Slurm job array:

#!/bin/bash

#SBATCH --partition=test

#SBATCH --constraint=dual

#SBATCH --ntasks=12

#SBATCH --cpus-per-task=1

#SBATCH --mem-per-cpu=2000

#SBATCH --time=00:05:00

#SBATCH --array=0-11:12

source /home/agburghardt/biswas/progs/Gromacs/bin/GMXRC

mydir=`pwd`

# Every 12-task block will be run on a separate node.

for I in $(seq 12); do

# This is the "global task number". Since we have an array of

# 192 tasks, J will range from 1 to 192.

J=$(($SLURM_ARRAY_TASK_ID+$I))

cd dir${J}

# Put each task into background, so that tasks are executed

# concurrently.

mdrun -nt 1 -v -deffnm sim &

#touch myfile

cd $mydir

# Wait a little before starting the next one.

#sleep 1

done

# Wait for all child processes to terminate.

wait

Multiple jobs:

#!/bin/bash

#SBATCH --ntasks=16

#SBATCH --time=01:10:00

#SBATCH --mem-per-cpu=4096

for i in `seq 1 $SLURM_NTASKS`

do

srun --nodes=1 --ntasks=1 --cpus-per-task=1 sh SINGLEJOB.slurm &

done

# IMPORTANT must wait for all to finish, or all get killed

wait

SCRIBBLES

AWK split file examples: http://www.theunixschool.com/2012/06/awk-10-examples-to-split-file-into.html
HP driver install for Ubuntu 18.04: https://askubuntu.com/questions/1058742/how-to-install-hp-printer-in-ubuntu-18-04
GRUB rescue: http://www.linuxandubuntu.com/home/ways-to-rescue-or-recover-grub-menu
python multiprocessing: https://sebastianraschka.com/Articles/2014_multiprocessing.html , https://stackoverflow.com/questions/40217873/multiprocessing-use-only-the-physical-cores
visualizing clusters in VMD: https://gromacs.bioexcel.eu/t/visualizing-clusters-of-molecules-with-trjconv-with-pbc/2946
My gnuplot settings:

#set size 0.9,1

# enable macros

set macros

# search for functions or data files in these directories

#set loadpath '/usr/local/lib/gnuplot'

set pal defined ( 0 '#000096', 1.5 '#0004ff', 3.5 '#0090ff', \

5.5 '#30ffc6', 6.0 '#94ff63', 7.5 '#ffe900', \

9.0 '#ff6400' , 10.5 '#d10000', 12 '#840000' )

#set border lw 3

#ERRORBARS CAP LENGTH

set bars 0.5

# add default line colors

#set style line 1 lc rgb '#0060ad' lt 1 lw 3 pt 5 # blue

#set style line 2 lc rgb '#dd181f' lt 1 lw 3 pt 7 # red

set style line 1 lc rgb "red" lt 1 lw 4

set style line 2 lc rgb "green" lt 1 lw 4

set style line 3 lc rgb "blue" lt 1 lw 4

set style line 4 lc rgb "cyan" lt 1 lw 4

set style line 5 lc rgb "violet" lt 1 lw 4

set style line 6 lc rgb "orange" lt 1 lw 4

set style line 7 lc rgb "black" lt 1 lw 4

set style line 10 lc rgb "#696969" lt 2 lw 6

# DOTTED

set style line 11 lc rgb "red" lt 2 lw 4 dt 3

set style line 12 lc rgb "green" lt 2 lw 4 dt 3

set style line 13 lc rgb "blue" lt 2 lw 4 dt 3

set style line 14 lc rgb "cyan" lt 2 lw 4 dt 3

set style line 15 lc rgb "violet" lt 2 lw 4 dt 3

set style line 16 lc rgb "orange" lt 2 lw 4 dt 3

set style line 17 lc rgb "black" lt 2 lw 4 dt 3

# POINTS

set style line 21 lc rgb "red" lt 1 pt -1 lw 2

set style line 22 lc rgb "green" lt 1 pt -1 lw 2

set style line 23 lc rgb "blue" lt 1 pt -1 lw 2

set style line 24 lc rgb "cyan" lt 1 pt -1 lw 2

set style line 25 lc rgb "violet" lt 1 pt -1 lw 2

set style line 26 lc rgb "orange" lt 1 pt -1 lw 2

set style line 27 lc rgb "black" lt 1 pt -1 lw 2

# ARROWS

set style arrow 1 nohead lc rgb "red" lt 0 lw 4

set style arrow 2 nohead lc rgb "green" lt 0 lw 4

set style arrow 3 nohead lc rgb "blue" lt 0 lw 4

set style arrow 4 nohead lc rgb "black" lt 0 lw 4

# add macros to select the desired line style

#BLUE = "1"

#RED = "2"

# points: 5/square, 7/circle, 9/triangle up

# add macros to select a desired terminal

WXT = "set terminal wxt size 350,262 enhanced font 'Verdana,10' \

persist"

EPS = "set terminal postscript eps enhanced color font 'Helvetica,24'"

PNG = "set terminal pngcairo size 350,262 enhanced font 'Verdana,10'"

SVG = "set terminal svg size 350,262 fname \

'Verdana, Helvetica, Arial, sans-serif' fsize = 10"

GROMACS wrap trajectory or remove rotation/translation

gmx trjconv -fit rot+trans -s prod1.tpr -n index.ndx -f prod1.xtc -o output.xtc

gmx editconf -ndef -f prod1.gro -n index.ndx -o prot_chol.gro

gmx trjconv -pbc mol -s prod1.tpr -n index.ndx -ur compact -center -f prod1.xtc -o output.xtc