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 = 5000
nstxout = 500
nstvout = 1
nstfout = 0
nstlog = 1
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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