<br><font class="Apple-style-span" size="3">Dear gmx-users:</font><div><font class="Apple-style-span" size="3">&nbsp;&nbsp; <font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">I got the waterbox simulation.It contains&nbsp;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">&nbsp;&nbsp; <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&nbsp;Zhao<br>Hefei&nbsp;National&nbsp;Laboratory&nbsp;for&nbsp;Physical&nbsp;Sciences&nbsp;at&nbsp;the&nbsp;Microscale,<br>University&nbsp;of&nbsp;Science&nbsp;and&nbsp;Technology&nbsp;of&nbsp;China,<br>Hefei,&nbsp;Anhui&nbsp;230026,&nbsp;China</span></div></div>