#!/bin/bash # # Code by venkentom@gmail.com # # Licenced by the GPL General Public License # Have a look at: # http://www.gnu.org/copyleft/gpl.html # For more information about the GPL License # # I am not responsible for what this code does to your hw/sw/mind # Use at your own risk # #Put gromacs commands after this line DIR=`pwd` #Config NPROCS=2 # Things to consider: -f is the CG input structure, -p is the AA topology! # separate topology for protein made using pdb2gmx: # pdb2gmx -f TM31C_sed.pdb -ignh (select CHARMM36!!) # lipids treated by CHARMM36 # water treated by CHARMM TIP3P model # use posre.itp and posre_popc.itp for position restrained during backwarding step # map_chol.sed: script needed to correct mapping files of cholesterol in Mapping/ (apparently due to different naming): chol.charmm36.map (make sure to delete old file!) # change ASP0 to ASPP, both when making topol (above) and in dynamic.gro!! sh initram.sh -f dynamic.gro -o system_aa.gro -to charmm36 -p topol_aa.top grompp -f emst.mdp -c system_aa.gro -p backmapped.top -o emst.tpr mdrun -deffnm emst -v -nt 4 editconf -f emst.gro -o emst.pdb #make_ndx -f emst.gro -o index.ndx <