[gmx-users] Coul-SR energy component - CG simulation

[Carlos Navarro Retamal]

Hi,
Just to update.
I tried to run a CG simulation having a mixture membrane composed by SQDG-MGDG-DGDG
and looking at the end of the .log file i found this:
  Epot (kJ/mol)        Coul-SR
Protein-Protein   -9.54302e+01
   Protein-SQDG   -3.40735e+00
   Protein-DGDG    0.00000e+00
   Protein-MGDG    0.00000e+00
  Protein-W_ION   -3.66900e+01
      SQDG-SQDG    7.59210e+00
      SQDG-DGDG    0.00000e+00
      SQDG-MGDG    0.00000e+00
     SQDG-W_ION   -7.42341e+01
      DGDG-DGDG    0.00000e+00
      DGDG-MGDG    0.00000e+00
     DGDG-W_ION    0.00000e+00
      MGDG-MGDG    0.00000e+00
     MGDG-W_ION    0.00000e+00
    W_ION-W_ION    3.77833e+00

So as you can see, the only energy reported were the ones describing the SQDG lipid membrane. And i don’t know what may be happening (for now i’m using the parameters reported by martini group in 2013    -> http://md.chem.rug.nl/cgmartini/index.php/glipids)
This is my *mdp file:
integrator               = md
dt                       = 0.01
nsteps                   = 50000000
nstcomm                  = 10
comm-grps =
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 10000
nstenergy                = 1000
nstxtcout                = 10000
xtc_precision            = 100
xtc-grps                 =
energygrps               = Protein SQDG DGDG MGDG W_ION
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4
cutoff-scheme            = group
coulombtype              = Shift  ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15 ; 2.5 (with polarizable water)
vdw_type                 = Shift  ;cutoff (for use with Verlet-pairlist)
rvdw_switch              = 0.9
rvdw                     = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl                   = v-rescale
tc-grps                  = Protein SQDG DGDG MGDG W_ION
tau_t                    = 1.0 1.0 1.0 1.0 1.0
ref_t                    = 320 320 320 320 320
Pcoupl                   = parrinello-rahman
Pcoupltype               = semiisotropic
tau_p                    = 12.0 12.0  ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility          = 3e-4  3e-4
ref_p                    = 1.0  1.0
gen_vel                  = no
gen_temp                 = 320
gen_seed                 = 473529
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 30
I tried with both, GROMACS 5.0.4 and 4.6.7 without luck
Best,
Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl



On March 26, 2015 at 4:32:18 PM, Carlos Navarro Retamal (cnavarro at utalca.cl<mailto:cnavarro at utalca.cl>) wrote:

Dear gromacs users,
I’m studying the interaction between protein and several mixture lipids (POPC-MGDG, POPC-DGDG, POPC-SQDG).
All simulations ran successfully.
Analysing the energy componentes during the simulations i noticed that when i calculated the Coul-SR energy componen Between the protein and each thylakoid membrane i got this:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-DGDG              0          0          0          0  (kJ/mol)

And that doesn’t have any sense. Looking into the simulation i noticed how the protein and membranes are interacting, so i don’t know what may be happening (the LJ-SR term showed a more favorable interaction with respect to the thylakoid lipid membrane rather than to the POPC membrane).
Is this normal? I’m really worried about these.
By the way, i’m using a shift potential to describe coulomb and vdw interactions (since martini force field was parametriced in that way),do you think that maybe this issue is because i’m not using PME to describe this interaction?
Best,
Carlos


--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl