<DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes">Dear all,</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes">I've run MD 500,000 steps (1000 ps). After the job ceased, i took the last configuration of structure (file: structure.gro), and ran MD more with the same input file. But i don't understand that why the properties of the last step of first MD is not equal to the zeroth step of the second MD. Below is the MD results of 1st MD and 2nd MD, respectively. And my MD paramerter file is as follow.</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes">Best regards</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=5><SPAN style="mso-spacerun: yes">Chiloo</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=4><SPAN style="mso-spacerun: yes">--------------------------------------------------------</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><I><FONT face="Angsana New"><STRONG><FONT size=4><SPAN style="mso-spacerun: yes"> </SPAN>Step<SPAN style="mso-spacerun: yes"> </SPAN>Time<SPAN style="mso-spacerun: yes"> </SPAN>Lambda<SPAN style="mso-spacerun: yes"> </SPAN>Annealing<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></STRONG></FONT></I></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><I><FONT face="Angsana New"><STRONG><FONT size=4><SPAN style="mso-spacerun: yes"> </SPAN>500000<SPAN style="mso-spacerun: yes"> </SPAN>1000.00006<SPAN style="mso-spacerun: yes"> </SPAN>0.00000<SPAN style="mso-spacerun: yes"> </SPAN>1.00000<o:p></o:p></FONT></STRONG></FONT></I></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Rel. Constraint Deviation:<SPAN style="mso-spacerun: yes"> </SPAN>Max<SPAN style="mso-spacerun: yes"> </SPAN>between atoms<SPAN style="mso-spacerun: yes"> </SPAN>RMS<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Before LINCS<SPAN style="mso-spacerun: yes"> </SPAN>0.067623<SPAN style="mso-spacerun: yes"> </SPAN>241<SPAN style="mso-spacerun: yes"> </SPAN>242<SPAN style="mso-spacerun: yes"> </SPAN>0.003032<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>After LINCS<SPAN style="mso-spacerun: yes"> </SPAN>0.000132<SPAN style="mso-spacerun: yes"> </SPAN>632<SPAN style="mso-spacerun: yes"> </SPAN>635<SPAN style="mso-spacerun: yes"> </SPAN>0.000012<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Energies (kJ/mol)<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Angle<SPAN style="mso-spacerun: yes"> </SPAN>Proper Dih. Ryckaert-Bell.<SPAN style="mso-spacerun: yes"> </SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">Improper Dih.<SPAN style="mso-spacerun: yes"> </SPAN>LJ-14<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>1.07364e+04<SPAN style="mso-spacerun: yes"> </SPAN>2.52571e+03<SPAN style="mso-spacerun: yes"> </SPAN>4.13630e+03<SPAN style="mso-spacerun: yes"> </SPAN>7.58160e+02<SPAN style="mso-spacerun: yes"> </SPAN>3.73031e+03<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><SPAN style="mso-spacerun: yes"> </SPAN></SPAN>Coulomb-14<SPAN style="mso-spacerun: yes"> </SPAN>LJ (SR)<SPAN style="mso-spacerun: yes"> </SPAN>Coulomb (SR)<SPAN style="mso-spacerun: yes"> </SPAN>Coulomb (LR)<SPAN style="mso-spacerun: yes"> </SPAN>Potential<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">1.98057e+04<SPAN style="mso-spacerun: yes"> </SPAN>6.58396e+02<SPAN style="mso-spacerun: yes"> </SPAN>-2.04387e+05<SPAN style="mso-spacerun: yes"> </SPAN>-1.00879e+05<SPAN style="mso-spacerun: yes"> </SPAN>-2.62915e+05<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><SPAN style="mso-spacerun: yes"> </SPAN>Kinetic En.<SPAN style="mso-spacerun: yes"> </SPAN></SPAN>Total Energy<SPAN style="mso-spacerun: yes"> </SPAN>Temperature Pressure (bar)<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>4.09683e+04<SPAN style="mso-spacerun: yes"> </SPAN>-2.21947e+05<SPAN style="mso-spacerun: yes"> </SPAN>3.10246e+02<SPAN style="mso-spacerun: yes"> </SPAN>1.66980e+02</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><I><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes">----------------------------------------------------------------- </SPAN></FONT></FONT></I></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><I><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN></FONT><FONT size=4><STRONG>Step<SPAN style="mso-spacerun: yes"> </SPAN>Time<SPAN style="mso-spacerun: yes"> </SPAN>Lambda<SPAN style="mso-spacerun: yes"> </SPAN>Annealing<o:p></o:p></STRONG></FONT></FONT></I></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><I><FONT face="Angsana New"><FONT size=4><STRONG><SPAN style="mso-spacerun: yes"> </SPAN>0<SPAN style="mso-spacerun: yes"> </SPAN>0.00000<SPAN style="mso-spacerun: yes"> </SPAN>0.00000<SPAN style="mso-spacerun: yes"> </SPAN>1.00000<o:p></o:p></STRONG></FONT></FONT></I></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Rel. Constraint Deviation:<SPAN style="mso-spacerun: yes"> </SPAN>Max<SPAN style="mso-spacerun: yes"> </SPAN>between atoms<SPAN style="mso-spacerun: yes"> </SPAN>RMS<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Before LINCS<SPAN style="mso-spacerun: yes"> </SPAN>0.067893<SPAN style="mso-spacerun: yes"> </SPAN>241<SPAN style="mso-spacerun: yes"> </SPAN>242<SPAN style="mso-spacerun: yes"> </SPAN>0.003031<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>After LINCS<SPAN style="mso-spacerun: yes"> </SPAN>0.000118<SPAN style="mso-spacerun: yes"> </SPAN>632<SPAN style="mso-spacerun: yes"> </SPAN>635<SPAN style="mso-spacerun: yes"> </SPAN>0.000011<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Energies (kJ/mol)<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Angle<SPAN style="mso-spacerun: yes"> </SPAN>Proper Dih. Ryckaert-Bell.<SPAN style="mso-spacerun: yes"> </SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">Improper Dih.<SPAN style="mso-spacerun: yes"> </SPAN>LJ-14<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>1.07468e+04<SPAN style="mso-spacerun: yes"> </SPAN>2.52814e+03<SPAN style="mso-spacerun: yes"> </SPAN>4.13693e+03<SPAN style="mso-spacerun: yes"> </SPAN>7.53671e+02<SPAN style="mso-spacerun: yes"> </SPAN>3.72928e+03<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><SPAN style="mso-spacerun: yes"> </SPAN></SPAN>Coulomb-14<SPAN style="mso-spacerun: yes"> </SPAN>LJ (SR)<SPAN style="mso-spacerun: yes"> </SPAN>Coulomb (SR)<SPAN style="mso-spacerun: yes"> </SPAN>Coulomb (LR)<SPAN style="mso-spacerun: yes"> </SPAN>Potential<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">1.98088e+04<SPAN style="mso-spacerun: yes"> </SPAN>6.62636e+02<SPAN style="mso-spacerun: yes"> </SPAN>-2.04375e+05<SPAN style="mso-spacerun: yes"> </SPAN>-1.00878e+05<SPAN style="mso-spacerun: yes"> </SPAN>-2.62887e+05<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><SPAN style="mso-spacerun: yes"> </SPAN>Kinetic En.<SPAN style="mso-spacerun: yes"> </SPAN></SPAN>Total Energy<SPAN style="mso-spacerun: yes"> </SPAN>Temperature Pressure (bar)<o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">4.09659e+04<SPAN style="mso-spacerun: yes"> </SPAN>-2.21921e+05<SPAN style="mso-spacerun: yes"> </SPAN>3.10227e+02<SPAN style="mso-spacerun: yes"> </SPAN>2.53964e+02<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT face="Angsana New"><FONT size=3><SPAN style="mso-spacerun: yes"> </SPAN>Step<SPAN style="mso-spacerun: yes"> </SPAN>Time<SPAN style="mso-spacerun: yes"> </SPAN>Lambda<SPAN style="mso-spacerun: yes"> </SPAN>Annealing<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New"><FONT size=3><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><SPAN style="mso-spacerun: yes"> </SPAN></SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.00200<SPAN style="mso-spacerun: yes"> </SPAN>0.00000<SPAN style="mso-spacerun: yes"> </SPAN>1.00000</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Angsana New" size=3>-----------------------------------------</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt">title = M2 in dmPC<BR>cpp = /lib/cpp<BR>constraints = all-bonds<BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 500000 ; total 1000 ps = 1 ns !<BR>nstcomm = 1<BR>nstxout = 250<BR>nstvout =
1000<BR>nstfout = 0<BR>nstlog = 100<BR>nstenergy = 100<BR>nstlist = 10<BR>ns_type = grid<BR>rlist = 1.2<BR>coulombtype = PME<BR>rcoulomb = 1.2<BR>rvdw = 1.2<BR>pbc = xyz<BR>; Berendsen temperature
coupling is on in two groups<BR>Tcoupl = berendsen<BR>tc-grps = Protein DMPC SOL Na<BR>tau_t = 0.1 0.1 0.1 0.1<BR>ref_t = 310 310 310 310<BR>; Energy monitoring<BR>energygrps = Protein DMPC SOL Na<BR>; Isotropic pressure coupling is now on<BR>Pcoupl = berendsen<BR>Pcoupltype =
isotropic<BR>tau_p = 1.0<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>; Generate velocites is off at 300 K.<BR>gen_vel = no<BR>gen_temp = 310.0<BR></P></DIV><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com