Brief instruction for PMF analysis of self-association of TM helical peptides.
This instruction illustrates how we analyzed the PMF profile of interaction between two TM peptides, using as an example 'CG-WALP19-oc' (the set #19b of our 2014 paper "Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: difference between atomistic and coarse-grained simulations" by M. Nishizawa and K. Nishizawa (2014) J Chem Phys ).
1. Please get a computer that runs Gromacs 4.x ready.
Download the zip file or its content (eight files): .gro, .top, .itp, .itp (Martini-v2.1), .itp (Martini-sol), .ndx, pre.mdp and run.mdp (named cg_w22.mdp) files. ( When you publish your results obtained using the Martini itp files above, please cite the Martini paper(s) by Marrink and coworkers. )
2. First, initial coordinates (gro files) that have various inter-helical distances have to be prepared. Do 'grompp' using the pre.mdp file and the above listed gro, top, itp files. Then, do 'mdrun' the obtained tpr file, which is a steered dynamics run that gradually brings the helices closer to each other ( from 2.2 nm to 0.4 nm).
3. Do trjconv against the .trr file obtained in 2. For this trjconv, we suggest to use " -sep -skip 10". This generates a series of gro files with inter-helical distances of 2.1nm, 2.0 nm, 1.9nm,.. and so on. Please rename the .gro files, including the number reflecting inter-helical distance in the name, like , such as, walp19_21.gro, walp19_20.gro, walp19_19.gro,... etc. For each of these gro files. do the following 4 and 5.
4. To make .tpr file, do grompp (e.g., grompp -f cg_22w.mdp -c walp19_21(and so on).gro -n *.ndx -p *.top -o walp19_21(and so on).tpr ). Of course, the 'pull_init1' value in the run.mdp file has to be altered in advance appropriately; this restrains the inter-helical distance (in nm) by the umbrella harmonic potential.
5. Run the tpr. ( e.g., mdrun -deffnm walp19_21(and so on).tpr -px pullx_walp19_21(and so on).xvg -pf pullf_walp19_21(and so on).xvg ) . If the peptide has popped out the octane slab, repeat the 4 and 5 with another set of the initial velocities.
6. Create a file named ' tpr-files_walp19.dat ', which is a list file of walp19_21(and so on).tpr. Also, create pullf-files_walp19.dat, which is a list file of pullf_walp19_21(and so on).xvg . To do so, enter one file name per line
Then do g_wham. (e.g., g_wham -it tpr-files_walp19.dat -if pullf-files_walp19.dat -o profile.xvg -hist hist.xvg -unit kJ -b 500000 -temp 323 -min 0.5 -max 2.3 )
Actually, by modifying the step 3, we generated and used 23 windows (inter-helical distances) in total: 0.6, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1.0,1.05, 1.1, 1.15, 1.2, 1.25, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2 nm.
For this set, we obtained a PMF curve with a depth of ~ 28.5 kJ/mol.