#!/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 #For TM31C_cholpopc2, let's move the peptide a bit up, to see if the C-terminus stays in the membrane, in contrast to TM31C_cholpopc! #We made the previous system using this: #./insane.py -f minimization_vaccum_rotate.gro -o system.gro -pbc optimal -box 6.6,6.6,11 -l POPC:7 -l CHOL:3 -u POPC:7 -u CHOL:3 -center -sol PW # but this puts the peptide simply in the center of the box #therefore first make the first make tpr file of our previous system grompp -f minimization.mdp -c system.gro -p system.top -o minimization.tpr #and then write out peptide conformation (gives error but writes out file anyway !) trjconv -s minimization.tpr -f system.gro -o system_peptide.gro #translate ze peptide editconf -f system_peptide.gro -translate 0 0 2 -noc -o system_peptide_new.gro #et voila, make new file (system_new.gro) using new coordinates for ze peptide in system_peptide_new.gro #et do ze grompp again for minimization grompp -f minimization.mdp -c system_new.gro -p system.top -o minimization.tpr mdrun -deffnm minimization -v -nt 4 #index file necessary to use as input with grompp, POPC_CHOL needs to be specified as one temperature coupling group, mdp files were modified accordingly make_ndx -f system.gro -o index.ndx <