<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt;color:#000000;"><DIV>Hello,</DIV>
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<DIV> I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD simulation. After the trajectories were complete, I ran g_lie on the trajectories for each case. Next, I subtracted the average ligand LIE from the average complex LIE for each case to get the interaction energy . Data is as follows:</DIV>
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<TD class=xl22 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; WIDTH: 68pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 13.2pt; BACKGROUND-COLOR: transparent" width=91 height=18></TD>
<TD class=xl22 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; WIDTH: 48pt; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" width=64><FONT face=Arial size=2><STRONG>Ligand 1</STRONG></FONT></TD>
<TD class=xl22 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; WIDTH: 48pt; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" width=64><FONT face=Arial size=2><STRONG>Ligand 2</STRONG></FONT></TD></TR>
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<TD class=xl23 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" x:num="-5.7350237060656459"><FONT face=Arial size=2> -5.7</FONT></TD>
<TD class=xl23 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" x:num="-8.8847332644808539"><FONT face=Arial size=2> -8.9</FONT></TD></TR>
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<TD class=xl22 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 13.2pt; BACKGROUND-COLOR: transparent" height=18><STRONG><FONT face=Arial size=2>St dev.</FONT></STRONG></TD>
<TD class=xl23 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" x:num="6.7072952041014346"><FONT face=Arial size=2> 6.7</FONT></TD>
<TD class=xl23 style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; BACKGROUND-COLOR: transparent" x:num="4.7103877706168049"><FONT face=Arial size=2> 4.7</FONT></TD></TR></TBODY></TABLE></DIV>
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<DIV>While the average energies themselves are reasonable, the st dev's seem to me to be too large - rendering the energy difference meaningless. I calculated the st. dev's based on the trajectories' g_lie values (in this case 1000 data points for a 1 ns run). I read in the tutorials that PME condition should not be used with g_lie, so I switched to cut-offs for my electrostatic forces. Is there anything else I might be missing? Again, I know the st. dev's are just too high to make g_lie useful so I blame myself for the initial setup. My .mdp file is below.</DIV>
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<DIV>Thanks, Marc</DIV>
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<P>; mdrun for C4AHL on unix parameters</P>
<P>title = trp_drg MD</P>
<P>cpp = /usr/bin/cpp ; location of cpp on linux</P>
<P>constraints = all-bonds</P>
<P>integrator = md</P>
<P>dt = 0.002 ; ps!</P>
<P>nsteps = 500000 ; total 1000 ps</P>
<P>nstcomm = 1</P>
<P>nstxout = 500 ; output coords every 1 ps</P>
<P>nstvout = 0</P>
<P>nstfout = 0</P>
<P>nstenergy = 500</P>
<P>nstlist = 10</P>
<P>ns_type = grid</P>
<P>pbc = xyz</P>
<P>rlist = 0.9</P>
<P>coulombtype = cut-off</P>
<P>rcoulomb = 1.2</P>
<P>vdwtype = cut-off</P>
<P>rvdw = 1.4</P>
<P>;fourierspacing = 0.12</P>
<P>;fourier_nx = 0</P>
<P>;fourier_ny = 0</P>
<P>;fourier_nz = 0</P>
<P>;pme_order = 6</P>
<P>;ewald_rtol = 1e-5</P>
<P>;optimize_fft = yes</P>
<P>; Berendsen temperature coupling is on in five groups</P>
<P>Tcoupl = berendsen</P>
<P>tau_t = 0.1 0.1</P>
<P>tc-grps = protein non-protein </P>
<P>ref_t = 300 300</P>
<P>; Use Energy group monitoring</P>
<P>energygrps = protein C6L OHY SOL Na+ </P>
<P>; Pressure coupling is on</P>
<P>Pcoupl = berendsen</P>
<P>pcoupltype = isotropic</P>
<P>tau_p = 1.0</P>
<P>compressibility = 4.5e-5</P>
<P>ref_p = 1.0</P>
<P>; Generate velocities is on at 300 K</P>
<P>gen_vel = yes</P>
<P>gen_temp = 300.0</P>
<P>gen_seed = -1</P>
<P>free_energy = yes</P></SPAN></DIV></div></body></html>