[gmx-users] undesired aggregation

Berk Hess gmx3 at hotmail.com
Tue Feb 16 15:13:29 CET 2010


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?


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

I was trying to simulate the behaviour of 
N-isopropyl propionamide, CH3-CH2-CO-NH-CH-(CH3)2 (NIPPA) in aqueous 
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 
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 
00133 Roma
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