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Hi,<br><br>This subject is extremely sensitive to force field and simulation accuracy.<br>The small forces driving aggregation are the result of many, large counteracting forces.<br>Force fields often give the right behavior, but nearly never at the correct temperature<br>unless they have been explicitly parametrized for this.<br><br>I would not expect the Gromos force field to behave too badly though,<br>since it has been parametrized to reproduce partitioning between water and cyclohexane.<br><br>What are your cut-off's and electrostatics settings?<br><br>Berk<br><br><hr id="stopSpelling">From: ester.chiessi@uniroma2.it<br>To: gmx-users@gromacs.org<br>Date: Tue, 16 Feb 2010 14:35:11 +0100<br>Subject: [gmx-users] undesired aggregation<br><br>
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<div><font face="Arial" size="2">Hi.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">I was trying to simulate the behaviour of
N-isopropyl propionamide, CH3-CH2-CO-NH-CH-(CH3)2 (NIPPA) in aqueous
solution.</font></div>
<div><font face="Arial" size="2">This molecule has an inverted solubility behaviour
with temperature and it displays a miscibility gap in water for temperatures
higher than about 30°C.</font></div>
<div><font face="Arial" size="2">Experiments show that at 293 K and 1 atm the
water/NIPPA omogeneous solution phase is stable at any composition.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">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].</font></div>
<div><font face="Arial" size="2">In the starting configuration the NIPPA molecules
were randomly placed and solvated.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">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.</font></div>
<div><font face="Arial" size="2">In a further run at 273 K ( a temperature
about 30 degrees lower than the critical temperature) I found the same
aggregation effect.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">What do you think? Am I beyond the possibilties of
the simulation?</font></div>
<div><font face="Arial" size="2">Any comment is welcome. Thanks in
advance</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">Ester</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">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.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2"></font> </div>
<div> </div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2">Ester Chiessi<br>Dipartimento di Scienze e
Tecnologie Chimiche<br>Università di Roma Tor Vergata<br>Via della Ricerca
Scientifica<br>00133 Roma<br><a href="http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm">http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm</a><br>tel:
*39*6*72594462</font></div>                                            <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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