[gmx-users] cluster fomation in triolein simulation

[Dallas Warren]

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.warren at 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-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of mahnam karim
Sent: Thursday, 7 June 2012 5:15 PM
To: gmx-users at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120607/555d93c1/attachment.html>