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<DIV><FONT face=Arial size=2><FONT size=3>Yes I'm using soft core
potentials:</FONT></FONT></DIV>
<DIV><FONT face=Arial>...</FONT></DIV>
<DIV><FONT face=Arial size=2>delta_lambda = 0.0<BR>sc-alpha = 1.5<BR>sc-sigma =
0.3<BR>...</FONT></DIV>
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<DIV><FONT face=Arial size=2><FONT size=3>Hi,<BR><BR>are you using soft core
portentials?<BR>Despite the theoretical drawbacks (see the previous discussion),
the<BR>creation/annihilation of atoms was impossible (in my experience) without
those<BR>potentials.<BR><BR>Regards.<BR><BR>Pedro.<BR><BR><BR>></FONT><FONT
size=3><I> Hi all.<BR></I>></FONT><FONT size=3><I> I'm trying FEP In
gromacs3.3. My system (3nm; 3nm; 3nm) consists<BR></I>></FONT><FONT
size=3><I> of one Na, Cl, DUM ion and solvent molecules.<BR></I>></FONT><FONT
size=3><I> During my free energy calculations I want to
perturb:<BR></I>></FONT><FONT size=3><I> 1) Cl- into
a DUM atom<BR></I>></FONT><FONT size=3><I> 2) DUM into
Cl-<BR></I>></FONT><I><BR></I><FONT size=3>></FONT><I><BR></I><FONT
size=3>></FONT><FONT size=3><I> I'm using ffgmx. I've added new
atom DUM into ffgmx.atp:<BR></I>></FONT><I><FONT size=3>
...<BR></DIV></FONT></I></FONT></BODY></HTML>