Hi Swapnil,

Did you try using an older version of Gromacs, say 3.3.1. If not just give it a try, may be it works. 

Hi Swapnil,

probably your initial structure is flawed or your equilibration protocol is bad. In the original paper they use a vesicle size of 8 nm in radius. Are you sure you built yours with 30 nm? Can you give us the maximum force after the minimization? Did you generate your mdp files yourself or by charmm-gui? 

@Kalpana: Gromacs versions older than 5.1 won't work as they do not support cylindrical restraints, needed for keeping the pores open until the vesicle has relaxed.

You should also look for answers in the MARTINI forum: http://md.chem.rug.nl/index.php/forum

Hi Eric,

Sorry for my late response.

I don't know if there is any problem with the initial structure because a DPPC vesicle generated from CHARMM-GUI is working fine. In the paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305359/) they say that the vesicle diameter is 600 A and for my project I need to build a vesicle of 15 nm radius (which is going fine if I use DPPC). The maximum forces are in order of 10^8-10^9. I use the mdp files from CHARMM-GUI only (but for the vesicles that I generated later with PACKMOL, I use my own mdp file and it gives me an another error "Software inconsistancy error"). I am just wondering why the DPPC vesicles works but the DLPC vesicles don't..!

Best,

Swapnil

@Kalpana, I tried running it with Gromacs-4 versions but it din't work. Later I found out what Eric said, it doesn't work for gromacs version older than 5.1

Here is the reference: http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Martini-Maker