[gmx-users] undesired aggregation
Ester Chiessi
ester.chiessi at uniroma2.it
Wed Feb 17 13:46:52 CET 2010
Thanks for your answer.
With the system [166 NIPPA and 4140 water molecules] I performed runs in three different modalities for the non-bonding interactions, as described in the following:
1)
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.2
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
2)
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = reaction_field
rcoulomb-switch = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 78.5
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
dispcorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
3) As 1) but with longer cut-offs
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.2
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.5
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
I observed aggregation in each case.
About the environment control, temperature had a RMSD of about 2.5 K and pressure of about 185 bar.
I was reading in the paper
J. Phys. Chem. B, 2003, 107 (35), pp 9424-9433
"Methodological Issues in Lipid Bilayer Simulations" by Céline Anézo,? Alex H. de Vries,? Hans-Dieter Höltje,? D. Peter Tieleman,§ and Siewert-Jan Marrink
that the Author modified some LJ parameters to enhance the hydration of some atoms in their system.
I do not know if it is a legitimate procedure, in my case. If I could obtain the 'right' behaviour of NIPPA at 293 K, should I be sure to use the same modified parameters at a different temperature?
Another idea is to try an all-atom force field, i.e. OPLS. Do you think anything could change?
Ester
----- Original Message -----
From: Berk Hess
To: Discussion list for GROMACS users
Sent: Tuesday, February 16, 2010 3:13 PM
Subject: RE: [gmx-users] undesired aggregation
Hi,
This subject is extremely sensitive to force field and simulation accuracy.
The small forces driving aggregation are the result of many, large counteracting forces.
Force fields often give the right behavior, but nearly never at the correct temperature
unless they have been explicitly parametrized for this.
I would not expect the Gromos force field to behave too badly though,
since it has been parametrized to reproduce partitioning between water and cyclohexane.
What are your cut-off's and electrostatics settings?
Berk
------------------------------------------------------------------------------
From: ester.chiessi at uniroma2.it
To: gmx-users at gromacs.org
Date: Tue, 16 Feb 2010 14:35:11 +0100
Subject: [gmx-users] undesired aggregation
Hi.
I was trying to simulate the behaviour of N-isopropyl propionamide, CH3-CH2-CO-NH-CH-(CH3)2 (NIPPA) in aqueous solution.
This molecule has an inverted solubility behaviour with temperature and it displays a miscibility gap in water for temperatures higher than about 30°C.
Experiments show that at 293 K and 1 atm the water/NIPPA omogeneous solution phase is stable at any composition.
I performed a few NPT MD simulations of NIPPA in water SPC using the 45A3 force field, at different NIPPA concentrations, 293 K (Nose Hoover) and 1 atm (Parrinello Rahman), PME for electrostatic. Two typical systems contained [288 NIPPA molecules and 1680 water molecules] or [166 NIPPA and 4140 water molecules].
In the starting configuration the NIPPA molecules were randomly placed and solvated.
I was very surprised to see that after 2 ns ( time step 2 fs) the NIPPA molecules aggregated, in several ways (layer, cylindrical tube, spherical object) depending on the NIPPA concentration, whereas I was expecting a complete solubility in water.
In a further run at 273 K ( a temperature about 30 degrees lower than the critical temperature) I found the same aggregation effect.
What do you think? Am I beyond the possibilties of the simulation?
Any comment is welcome. Thanks in advance
Ester
P.S. I found in the literature that the DPPC self-assembly was modeled in MD simulations ( de Vries et al JACS 2004) at 323 K, a temperature higher than the transition temperature of DPPC. Why did the Authors use a T where the organized phase is unstable? I was wondering since also for my system the temperature is a crucial parameter.
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
00133 Roma
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
tel: *39*6*72594462
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