In God We Trust Hello Dear gmx-users I want to simulate oliver oil by Gromacs. I made topology of triolein with G45a3 force field at NPT ensemble (according to SCHULER paper ; Journal of Computational Chemistry, Vol. 22, No. 11, 1205–1218 (2001). I generated a box with 216 triolein molecules that had random orientation by genconf and used it as starting structure. After minimization and 50 ps MD simulation, system become coagulate and some clusters were formed, Is it normal for triolein?.What is my wrong?.Here is my mdp file: nvt.mdp: title = n.pdb warnings = 10 cpp = /lib/cpp constraints = none integrator = md dt = 0.001 nsteps = 50000000 nstxout = 500 nstvout = 10000 nstfout = 0 nstlog = 10000 nstenergy = 1000 nstcalcenergy = 10 nstlist = 5 ns_type = grid rlist = 0.8 coulombtype = PME vdw-type = shift rcoulomb = 0.8 rvdw = 1.4 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes energygrps = DRG ; check charge groups and energy groups! fourierspacing = 0.1 rlistlong = 1.6
; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 tc-grps = DRG ref_t = 300 ; Pressure coupling is on Pcoupl = no tau_p = 0.1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thank you very much for your help. Yours truly Karim Mahnam (PhD, Assistant Professor) Biology Dept., Faculty of Sciences, Shahrekod University, IRAN. Tel. 098-0381-4424407 Fax. 098-0381-4424419
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