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rsync at remote server
without password: ssh-keygen [WITHOUT entering any passphrase] ssh-copy-id user@remote-host (example: ssh-copy-id altair) nohup rsync...
Mohd Athar
Mar 21, 20231 min read
install rdkit with jupyter notebook
Here are the quick commands, you need to make sure right python version: also note that rdkit need separate conda environment,...
Mohd Athar
Dec 7, 20221 min read
Autodock docking analysis: convert dlg to pdb
ligand output poses of the autodock can be converted into the pdb by the following bash code (available at dlg2pdb/dlg2pdb.sh at master ·...
Mohd Athar
Dec 6, 20221 min read
how to switch display manager
Switch Display Manager in Ubuntu 20.04 - TechPiezo
Mohd Athar
Jul 22, 20211 min read
for nvidia driver installation
How to Install Nvidia Drivers on Ubuntu 20.04 | Linuxize How to Install Nvidia Drivers on Ubuntu 20.04 | Linuxize
Mohd Athar
Jul 22, 20211 min read
How can I find out how much space my home directory is occupying?
How can I find out how much space my home directory is occupying? | Paul G. Allen School of Computer Science & Engineering...
Mohd Athar
Jul 22, 20212 min read
Useful commands to check linux configuration
FOR THE GPU CARD, if available nvidia-smi lshw -c memory sudo lshw -c memory free -g cat /proc/cpuinfo FOR MEMORY DETAILS/STICKWISE sudo...
Mohd Athar
Jul 11, 20211 min read
Selection Criteria of the thermodynamic ensemble in molecular dynamics simulation
MD have three different stages, minimisation, equilibrium and production run, and it all depend on the user what he want from these MD...
Mohd Athar
May 20, 20214 min read
Installation of AMBERTOOLS, ACPYPE
https://youtu.be/peMLSFIuUaUhttps://youtu.be/peMLSFIuUaU
Mohd Athar
May 16, 20211 min read
Extend Gromacs Simulation
To extend simulation to 50ns more, just run these two commands gmx convert-tpr -s md_0_1.tpr -extend 50000 -o md_1_2.tpr gmx mdrun...
Mohd Athar
May 8, 20211 min read
TOMCAT INSTALLATION (pc to server)
https://www.vultr.com/docs/how-to-install-apache-tomcat-8-on-centos-7 **for checking the running java file netstat -pant | grep "8080"...
Mohd Athar
May 8, 20211 min read
Antechamber: Amber to Gromacs Ligand topology
Antechamber $AMBERHOME/exe/antechamber -i *.pdb -fi pdb -o *.mol2 -fo mol2 -c bcc -s 2 $AMBERHOME/exe/parmchk -i sustiva.mol2 -f mol2 -o...
Mohd Athar
May 8, 20211 min read
Schrodinger gbsa via command
prime gbsa from trajectory #$SCHRODINGER/run python /opt/schrodinger2018-1/mmshare-v4.1/python/common/thermal_mmgbsa.py...
Mohd Athar
May 8, 20211 min read
Pymol select residues types and highlight
select hydrophilics,(resn arg+lys+his+glu+asp+asn+gln+thr+ser+cys) show sticks, (hydrophilics and !name c+n+o) color green,hydrophilics...
Mohd Athar
May 8, 20211 min read
MOE similarity analysis
MOE (for duplicates) db_nb_mols_incommon [dbv_KeyList[], 'MatrixOut.txt'] MOE (for similarity) 85% Similarity in database...
Mohd Athar
May 8, 20211 min read
g_mmpbsa gromacs plug in
#################g_mmpbsa##################################################### ../../../g_mmpbsa/bin/g_mmpbsa -f...
Mohd Athar
May 8, 20211 min read
Useful commands for Gromacs Post MD Analysis
############TO CHECK THE TRJ############################## gmx_mpi check -f md_0_1.xtc ##################################################...
Mohd Athar
May 8, 20211 min read
Job Scheduler PBS scripts
#!/bin/bash -l #$ -S /bin/bash #$ -cwd ##Move to current working directory #$ -V ## Running array job over all files in the models...
Mohd Athar
May 8, 20212 min read
Grinn software: Calculate residue wise contribution from Gromacs MD
copy all .itp and .mdp files to one folder. You can extract last 5-2 ns frames in .xtc file (via following commands) and ran the...
Mohd Athar
May 8, 20211 min read
How to calculate binding energy using Gaussian 09?
In gaussian16, they have automate the binding energy calculations, you just need to run single point calculation with counterpoise...
Mohd Athar
Sep 15, 20181 min read
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