Honghui Zhang

Honghui Zhang

PHD from CUHKSZ, specialised in biological science

Installation of Other Ordinary Software

Installation of pymol

Dependencies:
	PyMOL-2.5.8_appveyor647-Linux-x86_64-py39.tar.bz2

tar -jxf PyMOL-2.5.8_appveyor647-Linux-x86_64-py39.tar.bz2
export PATH=$PATH:/soft/pymol
export OMP_NUM_THREADS=32

Installation of VMD

Dependencies:
	vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz

tar -xvf vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
cd vmd-1.9.4a55
./configure LINUXAMD64
cd src

then change the installation directory /usr/local/lib/vmd to /soft/lib/vmd change the /usr/local/bin to soft/vmd/bin

make install
export PATH=$PATH:/soft/vmd-1.9.4a55/bin

Installation of Multiwfn

Dependencies:
	Multiwfn_3.8_dev_bin_Linux.zip, Xbin.tgz, motif-2.3.4-1.x86_64_0.rpm

tar zxf Xbin.tgz
unzip Multiwfn_3.8_dev_bin_Linux.zip
rpm2cpio motif-2.3.4-1.x86_64_0.rpm | cpio -div

then change the src

# For Memory (remove the the stack limit)
export OMP_STACKSIZE=200M
ulimit -s unlimited
 
#Multiwfn
export Multiwfnpath=/share/home/soft/Multiwfn_3.8_dev_bin_Linux
export PATH=$PATH:/share/home/soft/Multiwfn_3.8_dev_bin_Linux
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/home/soft/usr/lib64

then copy lib64 of Xbin to the lib64 of motif chomod 777 Multiwfn

Installation of molaris

Dependencies:
	Chen_huge.tgz, molaris_chen.tgz

tar xvf Chen_huge.tgz
tar xvf molaris_chen.tgz

then substitude molaris_hpc9.15_huge with Chen then create molaris_rc under soft file

export MOLARIS_PATH=/soft/molaris
export PATH="$MOLARIS_PATH/bin:$PATH"
export LD_LIBRARY_PATH=/soft/molaris/lib
export AMINO_LIB=/soft/molaris/lib/amino98.lib
export PARM_LIB=/share/home/grp-hiraoh/honghuizhang/soft/molaris/lib/parm.lib
export EVB_LIB=/soft/molaris/lib/evb.lib
export SOLVENT_OPT=/soft/molaris/lib/solvent.opt
export OUT_DIR=.

then add the environment variable to bash_rpofile

source /share/home/grp-hiraoh/honghuizhang/soft/molaris_rc

test with run.lsf

#!/bin/bash
#
#BSUB -J JOB
#BSUB -R "span[hosts=1]"
#BSUB -W 8:00
#BSUB -o stdout_%J.out
#BSUB -e stderr_%J.err
source ~/.bash_profile

export LD_LIBRARY_PATH=g/soft/molaris/lib
module load intel/2019.5 mpi/intel/2019.5 gcc/8.3.0


~/soft/molaris/bin/molaris_hpc9.15_huge <convert.inp> convert.log