This is a quick guideline to do a quick NAMD simulation

This notebook is created by Quantao Sun (quantaosun@gmail.com) for the purpose of molecular dynamic of a protein-ligand simulation.

Download the software NAMD. Note NAMD is a licensed software, you need to register to use it. If you just need to run a normal MD, the Linux-x86_64-multicore-CUDA version looks good, if you need to run replica exchange, then you need the multile-copy algorithum version, i.e., the netlrts version.

In [1]:
# Download the NAMD binary
!wget https://www.ks.uiuc.edu/Research/namd/2.14/download/94618/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz

--2021-04-24 09:14:29--  https://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz
Resolving www.ks.uiuc.edu (www.ks.uiuc.edu)... 130.126.120.43
Connecting to www.ks.uiuc.edu (www.ks.uiuc.edu)|130.126.120.43|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 169669114 (162M) [application/x-gzip]
Saving to: ‘NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz’

NAMD_2.14_Linux-x86 100%[===================>] 161.81M  26.1KB/s    in 2h 12m  

2021-04-24 11:26:34 (20.9 KB/s) - ‘NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz’ saved [169669114/169669114]
In [2]:
# Extract the file
# !tar -zxf /content/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz
!tar -zxf NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz

Please add the charmm gui files to dataset of the AI studio dataset. If you directly upload the charmm gui input as a file, you need to modify the next line path.

In [1]:
%cd /home/aistudio/data/data87836/

/home/aistudio/data/data87836
In [2]:
! tar -xzvf charmm-gui-for-namd-solution.tgz

charmm-gui-2062527065/3htb.cif
charmm-gui-2062527065/3htb_hetc.crd
charmm-gui-2062527065/3htb_hetc.pdb
charmm-gui-2062527065/3htb_proa.crd
charmm-gui-2062527065/3htb_proa.pdb
charmm-gui-2062527065/addCrystPdb.py
charmm-gui-2062527065/checkfft.py
charmm-gui-2062527065/checkfft.str
charmm-gui-2062527065/crystal_image.str
charmm-gui-2062527065/glycan.yml
charmm-gui-2062527065/input.config.dat
charmm-gui-2062527065/step1_crystal.info2
charmm-gui-2062527065/step1_crystal.pdb
charmm-gui-2062527065/step1_crystal.str
charmm-gui-2062527065/step1_pdbreader.crd
charmm-gui-2062527065/step1_pdbreader.inp
charmm-gui-2062527065/step1_pdbreader.out
charmm-gui-2062527065/step1_pdbreader.pdb
charmm-gui-2062527065/step1_pdbreader.psf
charmm-gui-2062527065/step1_pdbreader.str
charmm-gui-2062527065/step1_unitcell.info
charmm-gui-2062527065/step2.1_waterbox.crd
charmm-gui-2062527065/step2.1_waterbox.inp
charmm-gui-2062527065/step2.1_waterbox.out
charmm-gui-2062527065/step2.1_waterbox.pdb
charmm-gui-2062527065/step2.1_waterbox.prm
charmm-gui-2062527065/step2.1_waterbox.str
charmm-gui-2062527065/step2.2_ions.crd
charmm-gui-2062527065/step2.2_ions.inp
charmm-gui-2062527065/step2.2_ions.out
charmm-gui-2062527065/step2.2_ions.pdb
charmm-gui-2062527065/step2.2_ions.prm
charmm-gui-2062527065/step2.2_ions.str
charmm-gui-2062527065/step2.2_ions_orient.crd
charmm-gui-2062527065/step2_solvator.crd
charmm-gui-2062527065/step2_solvator.inp
charmm-gui-2062527065/step2_solvator.out
charmm-gui-2062527065/step2_solvator.pdb
charmm-gui-2062527065/step2_solvator.psf
charmm-gui-2062527065/step2_solvator.str
charmm-gui-2062527065/step3_pbcsetup.crd
charmm-gui-2062527065/step3_pbcsetup.inp
charmm-gui-2062527065/step3_pbcsetup.oldpsf
charmm-gui-2062527065/step3_pbcsetup.out
charmm-gui-2062527065/step3_pbcsetup.pdb
charmm-gui-2062527065/step3_pbcsetup.psf
charmm-gui-2062527065/step3_pbcsetup.str
charmm-gui-2062527065/step4_equilibration.inp
charmm-gui-2062527065/step5_production.inp
charmm-gui-2062527065/toppar.str
charmm-gui-2062527065/water_tmp.crd
charmm-gui-2062527065/jz4
charmm-gui-2062527065/jz4/ligandrtf.py
charmm-gui-2062527065/jz4/jz4.rtf
charmm-gui-2062527065/jz4/jz4.prm
charmm-gui-2062527065/jz4/JZ4.mol2
charmm-gui-2062527065/jz4/jz4.mol
charmm-gui-2062527065/jz4/jz4_g.rtf
charmm-gui-2062527065/jz4/JZ4.sdf
charmm-gui-2062527065/jz4/ndihe.str
charmm-gui-2062527065/namd
charmm-gui-2062527065/namd/step3_input.pdb
charmm-gui-2062527065/namd/step5_production.inp
charmm-gui-2062527065/namd/step3_input.crd
charmm-gui-2062527065/namd/step3_input.psf
charmm-gui-2062527065/namd/restraints
charmm-gui-2062527065/namd/restraints/prot_posres.ref
charmm-gui-2062527065/namd/README
charmm-gui-2062527065/namd/sysinfo.dat
charmm-gui-2062527065/namd/toppar
charmm-gui-2062527065/namd/toppar/toppar_all36_polymer_solvent.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_bacterial.str
charmm-gui-2062527065/namd/toppar/toppar_all36_carb_glycolipid.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_sphingo.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_cholesterol.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_retinol.str
charmm-gui-2062527065/namd/toppar/toppar_all36_na_rna_modified.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_mycobacterial.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_lps.str
charmm-gui-2062527065/namd/toppar/toppar_all36_carb_glycopeptide.str
charmm-gui-2062527065/namd/toppar/par_all36_na.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_na_combined.str
charmm-gui-2062527065/namd/toppar/par_all36_cgenff.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_miscellaneous.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_c36m_d_aminoacids.str
charmm-gui-2062527065/namd/toppar/toppar_water_ions.str
charmm-gui-2062527065/namd/toppar/jz4.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_yeast.str
charmm-gui-2062527065/namd/toppar/par_all36m_prot.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_lnp.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_detergent.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_prot.str
charmm-gui-2062527065/namd/toppar/toppar_all36_carb_imlab.str
charmm-gui-2062527065/namd/toppar/toppar_all36_nanolig_patch.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_arg0.str
charmm-gui-2062527065/namd/toppar/par_interface.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_cardiolipin.str
charmm-gui-2062527065/namd/toppar/toppar_dum_noble_gases.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_heme.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_model.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_inositol.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_ether.str
charmm-gui-2062527065/namd/toppar/toppar_all36_nano_lig.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_archaeal.str
charmm-gui-2062527065/namd/toppar/toppar_all36_synthetic_polymer_patch.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_modify_res.str
charmm-gui-2062527065/namd/toppar/toppar_all36_synthetic_polymer.str
charmm-gui-2062527065/namd/toppar/toppar_all36_label_spin.str
charmm-gui-2062527065/namd/toppar/toppar_ions_won.str
charmm-gui-2062527065/namd/toppar/par_all36_lipid.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_label_fluorophore.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_tag.str
charmm-gui-2062527065/namd/toppar/toppar_all36_prot_fluoro_alkanes.str
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_hmmm.str
charmm-gui-2062527065/namd/toppar/par_all36_carb.prm
charmm-gui-2062527065/namd/toppar/toppar_all36_lipid_dag.str
charmm-gui-2062527065/namd/toppar/toppar_all36_na_nad_ppi.str
charmm-gui-2062527065/namd/step4_equilibration.inp
charmm-gui-2062527065/toppar
charmm-gui-2062527065/toppar/toppar_all36_polymer_solvent.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_bacterial.str
charmm-gui-2062527065/toppar/top_all36_lipid.rtf
charmm-gui-2062527065/toppar/toppar_all36_carb_glycolipid.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_sphingo.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_cholesterol.str
charmm-gui-2062527065/toppar/toppar_all36_prot_retinol.str
charmm-gui-2062527065/toppar/toppar_all36_na_rna_modified.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_mycobacterial.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_lps.str
charmm-gui-2062527065/toppar/top_all36_prot.rtf
charmm-gui-2062527065/toppar/toppar_all36_carb_glycopeptide.str
charmm-gui-2062527065/toppar/par_all36_na.prm
charmm-gui-2062527065/toppar/top_interface.rtf
charmm-gui-2062527065/toppar/toppar_all36_prot_na_combined.str
charmm-gui-2062527065/toppar/par_all36_cgenff.prm
charmm-gui-2062527065/toppar/toppar_all36_lipid_miscellaneous.str
charmm-gui-2062527065/toppar/toppar_all36_prot_c36m_d_aminoacids.str
charmm-gui-2062527065/toppar/toppar_water_ions.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_yeast.str
charmm-gui-2062527065/toppar/top_all36_carb.rtf
charmm-gui-2062527065/toppar/par_all36m_prot.prm
charmm-gui-2062527065/toppar/toppar_all36_lipid_lnp.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_detergent.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_prot.str
charmm-gui-2062527065/toppar/toppar_all36_carb_imlab.str
charmm-gui-2062527065/toppar/toppar_all36_nanolig_patch.str
charmm-gui-2062527065/toppar/toppar_all36_prot_arg0.str
charmm-gui-2062527065/toppar/par_interface.prm
charmm-gui-2062527065/toppar/toppar_all36_lipid_cardiolipin.str
charmm-gui-2062527065/toppar/toppar_dum_noble_gases.str
charmm-gui-2062527065/toppar/toppar_all36_prot_heme.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_model.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_inositol.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_ether.str
charmm-gui-2062527065/toppar/toppar_all36_nano_lig.str
charmm-gui-2062527065/toppar/top_all36_cgenff.rtf
charmm-gui-2062527065/toppar/toppar_all36_lipid_archaeal.str
charmm-gui-2062527065/toppar/toppar_all36_synthetic_polymer_patch.str
charmm-gui-2062527065/toppar/toppar_all36_prot_modify_res.str
charmm-gui-2062527065/toppar/toppar_all36_synthetic_polymer.str
charmm-gui-2062527065/toppar/toppar_all36_label_spin.str
charmm-gui-2062527065/toppar/tip216.crd
charmm-gui-2062527065/toppar/toppar_ions_won.str
charmm-gui-2062527065/toppar/par_all36_lipid.prm
charmm-gui-2062527065/toppar/toppar_all36_label_fluorophore.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_tag.str
charmm-gui-2062527065/toppar/top_all36_na.rtf
charmm-gui-2062527065/toppar/toppar_all36_prot_fluoro_alkanes.str
charmm-gui-2062527065/toppar/toppar_all36_lipid_hmmm.str
charmm-gui-2062527065/toppar/par_all36_carb.prm
charmm-gui-2062527065/toppar/toppar_all36_lipid_dag.str
charmm-gui-2062527065/toppar/toppar_all36_na_nad_ppi.str
In [3]:
%cd charmm-gui-2062527065

/home/aistudio/data/data87836/charmm-gui-2062527065
In [9]:
!ls

3htb.cif	     step1_pdbreader.out      step2_solvator.crd
3htb_hetc.crd	     step1_pdbreader.pdb      step2_solvator.inp
3htb_hetc.pdb	     step1_pdbreader.psf      step2_solvator.out
3htb_proa.crd	     step1_pdbreader.str      step2_solvator.pdb
3htb_proa.pdb	     step1_unitcell.info      step2_solvator.psf
addCrystPdb.py	     step2.1_waterbox.crd     step2_solvator.str
checkfft.py	     step2.1_waterbox.inp     step3_pbcsetup.crd
checkfft.str	     step2.1_waterbox.out     step3_pbcsetup.inp
crystal_image.str    step2.1_waterbox.pdb     step3_pbcsetup.oldpsf
glycan.yml	     step2.1_waterbox.prm     step3_pbcsetup.out
input.config.dat     step2.1_waterbox.str     step3_pbcsetup.pdb
jz4		     step2.2_ions.crd	      step3_pbcsetup.psf
namd		     step2.2_ions.inp	      step3_pbcsetup.str
step1_crystal.info2  step2.2_ions_orient.crd  step4_equilibration.inp
step1_crystal.pdb    step2.2_ions.out	      step5_production.inp
step1_crystal.str    step2.2_ions.pdb	      toppar
step1_pdbreader.crd  step2.2_ions.prm	      toppar.str
step1_pdbreader.inp  step2.2_ions.str	      water_tmp.crd
In [6]:
%%bash
cd namd
ls

README
restraints
step3_input.crd
step3_input.pdb
step3_input.psf
step4_equilibration.inp
step5_production.inp
sysinfo.dat
toppar
In [7]:
!pwd

/home/aistudio/data/data87836/charmm-gui-2062527065
In [8]:
%cd namd/

/home/aistudio/data/data87836/charmm-gui-2062527065/namd
In [12]:
!pwd

/home/aistudio/data/data87836/charmm-gui-2062527065/namd
In [13]:
# run NAMD. You should change the paths to correspond to the files 
! /home/aistudio/NAMD_2.14_Linux-x86_64-multicore-CUDA/namd2  step4_equilibration.inp > step4.log
In [14]:
!pwd

/home/aistudio/data/data87836/charmm-gui-2062527065/namd

The production takes about 2 hours to finish if you have not modified the configuration file, feel free to extend the running steps for a longer simulation.

In [11]:
# run NAMD. You should change the paths to correspond to the files
! /home/aistudio/NAMD_2.14_Linux-x86_64-multicore-CUDA/namd2 step5_production.inp > step5.log

Use next section if you have multiple dcd files

In [ ]:
# Download CatDCD to combine the dcd files into1.log
#!wget https://www.ks.uiuc.edu/Development/MDTools/catdcd/files/catdcd-4.0b.tar.gz
#!tar -zxf catdcd-4.0b.tar.gz
In [ ]:
# Run CatDCD. follow the instructions
#!/content/LINUX/bin/catdcd4.0/catdcd
In [ ]: