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<DIV><FONT face=Courier>Hi all,</FONT></DIV>
<DIV><FONT face=Courier></FONT> </DIV>
<DIV><FONT face=Courier>I'm doing a simulation on a small protein. The protein
is very unstabel in the simulation and the rmsd after ~ 40 ns is already 0.6 nm
for the backbone atoms. I am using the gromos force field.</FONT></DIV>
<DIV><FONT face=Courier>This really makes me wonder if any of the mdp-parameters
is very wrong cause the temperature is really low. Probably there is something
wrong with the non-bonded interactions?</FONT></DIV>
<DIV><FONT face=Courier></FONT> </DIV>
<DIV><FONT face=Courier>here are the mdp-options:</FONT></DIV>
<DIV><FONT face=Courier></FONT> </DIV>
<DIV>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>cpp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>/lib/cpp<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-com:office:office"
/><o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>constraints<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>all-bonds<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>integrator<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>md<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>dt<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.002<SPAN
style="mso-spacerun: yes">
</SPAN>;# ps !<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nsteps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1000000<SPAN
style="mso-spacerun: yes"> </SPAN>;# total 2
ns<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>tinit<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> 0</SPAN></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>;# frequency for
center of mass motion removal<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstcomm<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>;#
output<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstxout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>100000<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstxtcout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>100<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>xtc_grps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>PROTEIN<SPAN
style="mso-spacerun: yes"> </SPAN>;# without
water<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstvout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>100000</FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstfout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>100000<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstlog<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>100<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstenergy<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>100<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>energygrps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>PROTEIN</FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> </FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>nstlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>5<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>ns_type<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>grid<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>rlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>0.8<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>;# non bonded
interactions<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>coulombtype<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>Reaction-Field<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>epsilon_r<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>54<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>rcoulomb<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.4<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>vdwtype<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>cut-off<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>rvdw<SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>0.8<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>;# Berendsen
temperature coupling is on in two groups<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>Tcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>berendsen<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>tau_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.1<SPAN
style="mso-spacerun: yes">
</SPAN>0.1<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>tc-grps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>PROTEIN<SPAN
style="mso-spacerun: yes"> </SPAN>SOL<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>ref_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> 278</SPAN><SPAN
style="mso-spacerun: yes"> 278</SPAN></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>;# pressure
coupling<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>Pcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>berendsen<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>tau_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>0.5<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier>compressibility<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>4.5e-5<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>ref_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.0<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT
face=Courier></FONT></SPAN> </P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>gen_vel<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> yes</SPAN></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"><FONT face=Courier>gen_temp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> 278</SPAN></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-fareast-font-family: 'MS Mincho'"></SPAN><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'MS Mincho'; mso-ansi-language: DE-CH; mso-fareast-language: DE; mso-bidi-language: AR-SA"><FONT
face=Courier>gen_seed<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> -1</SPAN></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'MS Mincho'; mso-ansi-language: DE-CH; mso-fareast-language: DE; mso-bidi-language: AR-SA"><SPAN
style="mso-spacerun: yes"><FONT face=Courier></FONT></SPAN></SPAN> </P>
<P class=MsoPlainText style="MARGIN: 0cm 0cm 0pt"><SPAN
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'MS Mincho'; mso-ansi-language: DE-CH; mso-fareast-language: DE; mso-bidi-language: AR-SA"><SPAN
style="mso-spacerun: yes"><!--StartFragment --><FONT
face=Courier> </FONT></P><PRE><FONT face=Courier>Thanks a lot in advance. Cheers,
Lukas</FONT></PRE></SPAN></SPAN></DIV></BODY></HTML>