[gmx-users] cluster fomation in triolein simulation

[mahnam karim]

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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