<br><font class="Apple-style-span" size="3">Dear gmx-users:</font><div><font class="Apple-style-span" size="3"> <font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">I got the waterbox simulation.It contains 895</span></font><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> water molecules.</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">the used force-field is amber03.</span></font></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><font class="Apple-style-span" size="3"> with the same topol.tpr file,</font></span></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> Simulation on CPU ,the 0-step p</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">otential Energy = -20846.187500 KJ/mol,</span></font></div><div><div><font class="Apple-style-span" size="3"> <span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">Simulation on GPU ,the 0-step p</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">otential Energy = -24478.279297 KJ/mol.</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> </span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">why these are so different?</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><br></span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">The input mdp file is:</span></font></div><div><font class="Apple-style-span" face="monospace" size="3"><span class="Apple-style-span" style="white-space: pre;">constraints = all-bonds
integrator = md-vv
dt = 0.002 ; ps !
nsteps = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = Reaction-Field-zero
vdwtype = shift
rcoulomb = 0.9
rvdw = 0.9
pbc = xyz
epsilon_rf = 0
comm_mode = linear
nstxout = 0
nstfout = 0
nstvout = 0
nstxtcout = 0
nstlog = 1
nstcalcenergy = -1
nstenergy = 1
energygrps = SOL
tcoupl = berendsen
tc-grps = system
tau-t = 0.1
ref-t = 300</span></font></div><div><font class="Apple-style-span" size="3"><br></font></div><div><span class="Apple-style-span" style="font-family: Simsun; "><font class="Apple-style-span" size="3"><pre>Yours sincerely,</pre><pre>Wenhui </pre></font></span><br><span><br>--<br>Wen-Hui Zhao<br>Hefei National Laboratory for Physical Sciences at the Microscale,<br>University of Science and Technology of China,<br>Hefei, Anhui 230026, China</span></div></div>