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

[Carlos Navarro Retamal]

Hi Justin,
Thanks a lot for your reply.
I do think about that, but i forgot to mention that i’ve ran simulation in the presence of POPC getting values of Could-SR, but the think is that i forgot that POPC posees both, a positive and a negative charge, so even been a ‘neutral’ molecule, is able to make electrostatic interactions :) (as well as SQDG as you already mentioned it) :)
Thanks again.
Best regards,
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 11:01:34 PM, Justin Lemkul (jalemkul at vt.edu<mailto:jalemkul at vt.edu>) wrote:


On 3/26/15 4:04 PM, Carlos Navarro Retamal wrote:
> 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)

MGDG and DGDG (if I have found the correct reference for the topologies) have no
charged beads, so there cannot be any Coulombic interactions involving these
molecules. SQDG has one negatively charged bead, so it has non-zero Coul-SR values.

-Justin

> 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
>

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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