[gmx-users] EM curve question

[parto haghighi]

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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