GROMACS version: gromacs-2023.1
Hi I am Anushka Garhwal, phd scholar IITG, Guwahati, India
I have run molecular dynamics (MD) simulations using GROMACS for a lysozyme system in both its apo form and in complex with a ligand, using the following parameters:
Force field: OPLS-AA, Water model: TIP3P, Ligand topology: Generated using SwissParam, Box type: Cubic, System setup: Energy minimization, followed by NVT and NPT equilibration, Production MD: 100 ns.
The simulations were carried out following the “Lysozyme in Water” tutorial for the apo system and the “Protein-Ligand Complex” tutorial for the complex system. I observed RMSD values around 0.36 nm for the apo form and between 0.4 and 0.5 nm for the complex.
Could someone please let me know:
Are these RMSD values considered acceptable for systems of this kind, especially for publication purposes?
Is the slightly higher RMSD in the complex form a cause for concern?
If not acceptable, what steps would you recommend troubleshooting or improve the setup?
I’ve attached the exact scripts used for both systems. If any further information is needed, I’d be happy to provide it.
#!/bin/bash
#SBATCH --job-name=one
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --partition=gpu
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out
#SBATCH --time=07-00:00:00
#SBATCH --gres=gpu:1
ulimit -s unlimited
ulimit -c unlimited
########################### Load Module as requirement ############################################
module load spack/0.17
. /home/apps/spack/share/spack/setup-env.sh
spack load gromacs@2023.1%gcc@=11.2.0 /sn3eh6g
source /home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/gromacs-2023.1-sn3eh6g7skaivgaznwnsmt5p22vaex2s/bin/GMXRC
############################################################################
################################# Command ########################################
cd /scratch/
#gmx_mpi pdb2gmx -f protein.pdb -o prot_processed.gro -water tip3p -ff oplsaa
#gmx_mpi editconf -f complex.pdb -o newbox.gro -bt cubic -d 1.0
#gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
#gmx_mpi grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
#echo “SOL”|gmx_mpi genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
#gmx_mpi grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 5
#gmx_mpi mdrun -v -deffnm em
#echo “> 0 & ! a H*” “> q”|gmx_mpi make_ndx -f lig.pdb -o index_lig.ndx
#echo “3”|gmx_mpi genrestr -f lig.pdb -n index_lig.ndx -o posre_lig.itp -fc 1000 1000 1000
#echo “1|13” “q”|gmx_mpi make_ndx -f em.gro -o index.ndx
#gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr -maxwarn 5
gmx_mpi mdrun -v -deffnm nvt
gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr -maxwarn 5
gmx_mpi mdrun -v -deffnm npt
gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr -maxwarn 5
gmx_mpi mdrun -deffnm md_0_1
echo “Protein” “System”|gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_nojump.xtc -center -pbc nojump -ur compact
#echo “Protein” “System”|gmx_mpi rms -s md_0_1.tpr -f md_0_1_nojump.xtc -o rmsd_ps1_nojump.xvg -tu ns
echo “Backbone” “Protein”|gmx_mpi rms -s md_0_1.tpr -f md_0_1_nojump.xtc -o rmsd_1nojump.xvg -tu ns
echo “Protein”|gmx_mpi gyrate -s md_0_1.tpr -f md_0_1_nojump.xtc -o gyrate_1nojump.xvg
echo “Backbone”|gmx_mpi rmsf -s md_0_1.tpr -f md_0_1_nojump.xtc -o rmsf_1nojump.xvg
gmx_mpi grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
gmx_mpi mdrun -deffnm ie -rerun md_0_1_nojump.xtc -nb cpu
echo “21 22 0”|gmx_mpi energy -f ie.edr -o interaction_energy.xvg
echo “4 4”|gmx_mpi covar -f md_0_1_nojump.xtc -s md_0_1.tpr
echo “4 4”|gmx_mpi anaeig -v eigenvec.trr -f md_0_1_nojump.xtc -eig eigenval.xvg -s md_0_1.tpr -first 1 -last 1 -nframes 100 -extr ev1.pdb
echo “4 4”|gmx_mpi anaeig -v eigenvec.trr -f md_0_1_nojump.xtc -eig eigenval.xvg -s md_0_1.tpr -first 2 -last 2 -nframes 100 -extr ev2.pdb
echo “4 4”|gmx_mpi anaeig -v eigenvec.trr -f md_0_1_nojump.xtc -eig eigenval.xvg -s md_0_1.tpr -first 1 -last 2 -2d 2pc.xvg
gmx_mpi sham -f 2pc.xvg -notime -ls gibbs.xpm
python3 xpm2mat.py gibbs.xpm gibbs.xvg