Triolein only? What is the density of your box? By coagulated, do you mean there is vacuum in the box?
Appears that all that has happened is you have placed insufficient number of molecules in the box to fill it entirely. You can either start by putting more molecules in the box or run the simulation with pressure coupling actually on, you have done NVT, not NPT as you have indicated. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mahnam karim Sent: Thursday, 7 June 2012 5:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] cluster fomation in triolein simulation 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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