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