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<DIV><FONT face=Arial size=2>Hello,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I tried for the first time the free energy
perturbation code and I am a little confused. I am convinced I make a mistake
somewhere but I cannot see where is it.</FONT></DIV>
<DIV><FONT face=Arial size=2>I simulate a polymer system and I want some atoms
in the simulation box to "dissapear"; this means to set the vdW, Coulomb and
bonded parameters to 0.0 in the state B for these atoms (Is this
right?).</FONT></DIV>
<DIV><FONT face=Arial size=2>When I use the topology .itp file without
specifying any parameters for state B, everything goes well, but when I
introduce the state B parameters for the atoms I want to "dissapear" the
simulations crash EVEN IF I "SET FREE_ENERGY = no" in the .mdp file. The grompp
program shouldn't ignore the state B parameters in this case and use the
"normal" ones (without any modification during the course of the
simulation)?</FONT></DIV>
<DIV><FONT face=Arial size=2>Anyway, as I said, even if I set the free_energy =
no in the .mdp file the simulation results differ from that obtained with a .mdp
file without any state B parameters specified and it crashes (using the same
starting structure)!</FONT></DIV>
<DIV><FONT face=Arial size=2>I don't know where I go wrong in setting the
parameters for free energy.</FONT></DIV>
<DIV><FONT face=Arial size=2>I will be very grateful if anyone can help me with
an advice concerning this problem.</FONT></DIV>
<DIV><FONT face=Arial size=2>Thank you very much,</FONT></DIV>
<DIV><FONT face=Arial size=2>Andrei</FONT></DIV></BODY></HTML>