Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) 2. Download lipid.itp file and make new force field for it (like second gromacs tutorial) 3. Use editconf and cat to prepare a system with 12 ligand in both sides of lipid. 4. Add wares 5 . Add 8 CL
[ molecules ] ; Compound #mols DRG 12 DMPC 128 SOL 1976 CL 12 5. Use these parameters in minim.mdp file: Integrator = steep emtol = 1000.0 emstep = 0.0001 nsteps = 50000 nstlist = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1 pbc = xyz Statistics over 397 steps [ 1.0000 through 397.0000 ps ], 1 data sets All statistics are over 319 points (frames) Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 6.00519e+09 5.5e+09 2.98259e+10 -3.30965e+10 (kJ/mol) Its value is positive and after: g_energy -f em.edr its curve converges to zero. Help me to correct its parameter if its possible. I have another question, should I do energy minimization after adding each ligand molecules to bilayer? Thanks in advance. P.Haghighi
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