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<DIV><FONT face="Times New Roman">gmx-users:</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Greetings gmx-users! I have come up
against a road block that I don't know how to surpass. Our system is a
simple DPPC monolayer consisting of 30 lipid molecules with no water. I
have been using the "S-peptide" section of "Getting Started" as a guide to get
my MD up and running. Now, when I try to energy minimize, I keep getting
results that leave the system unchanged:</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT size=2><FONT
face="Courier New">Steepest Descents:<BR><SPAN
style="mso-spacerun: yes"> </SPAN>Tolerance<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>2.00000e+03<BR><SPAN
style="mso-spacerun: yes"> </SPAN>Number of steps<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes">
</SPAN>200<BR>Step=<SPAN style="mso-spacerun: yes"> </SPAN>0,
Dmax= 1.0e-02 nm, Epot=<SPAN style="mso-spacerun: yes"> </SPAN>7.02686e+04
Fmax= 5.87704e+05, atom= 31<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>1, Dmax= 1.0e-02 nm,
Epot=<SPAN style="mso-spacerun: yes"> </SPAN>3.51496e+04 Fmax=
1.68366e+05, atom= 31<BR>Step=<SPAN style="mso-spacerun: yes">
</SPAN>2, Dmax= 1.2e-02 nm, Epot=<SPAN style="mso-spacerun: yes">
</SPAN>1.93629e+04 Fmax= 5.30734e+04, atom= 1497<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>3, Dmax= 1.4e-02 nm,
Epot=<SPAN style="mso-spacerun: yes"> </SPAN>1.14356e+04 Fmax=
1.37348e+04, atom= 31<BR>Step=<SPAN style="mso-spacerun: yes">
</SPAN>4, Dmax= 1.7e-02 nm, Epot=<SPAN style="mso-spacerun: yes">
</SPAN>5.40411e+03 Fmax= 6.98762e+03, atom= 1498<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>5, Dmax= 2.1e-02 nm,
Epot=<SPAN style="mso-spacerun: yes"> </SPAN>2.42665e+03 Fmax=
4.88417e+03, atom= 1197<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>7, Dmax= 1.2e-02 nm,
Epot=<SPAN style="mso-spacerun: yes"> </SPAN>1.93304e+03 Fmax=
5.89898e+03, atom= 184<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>9, Dmax= 7.5e-03 nm,
Epot=<SPAN style="mso-spacerun: yes"> </SPAN>9.61426e+02 Fmax=
3.05110e+03, atom= 184<BR>Step=<SPAN style="mso-spacerun: yes">
</SPAN>11, Dmax= 4.5e-03 nm, Epot=<SPAN style="mso-spacerun: yes">
</SPAN>6.04071e+02 Fmax= 2.58888e+03, atom= 184<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>12, Dmax= 5.4e-03 nm, Epot=<SPAN
style="mso-spacerun: yes"> </SPAN>4.29385e+02 Fmax= 3.75457e+03, atom=
184<BR>Step=<SPAN style="mso-spacerun: yes"> </SPAN>13, Dmax=
6.4e-03 nm, Epot=<SPAN style="mso-spacerun: yes"> </SPAN>2.63337e+02 Fmax=
4.23455e+03, atom= 184<BR>Step=<SPAN style="mso-spacerun: yes">
</SPAN>14, Dmax= 7.7e-03 nm, Epot=<SPAN style="mso-spacerun: yes">
</SPAN>2.26982e+02 Fmax= 5.06575e+03, atom= 184<BR>Step=<SPAN
style="mso-spacerun: yes"> </SPAN>16, Dmax= 4.6e-03 nm, Epot=
-3.13108e+02 Fmax= 1.05358e+03, atom= 1231<BR><BR>writing lowest energy
coordinates.<BR><BR>Steepest Descents converged to 2000 in 17 steps<BR><SPAN
style="mso-spacerun: yes"> </SPAN>Potential Energy<SPAN
style="mso-spacerun: yes"> </SPAN>= -3.13108e+02<BR>Maximum force:<SPAN
style="mso-spacerun: yes"> </SPAN>1.05358e+03</FONT></FONT></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT size=2><FONT
face="Courier New"><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"><o:p>I would expect the EM process to run a much longer
time; here it only takes a couple of seconds. Could the simulation be
examining only select atoms? Should the file "em.mdp" be modified to make
the minimization process more thorough? Any help you can provide will be
appreciated.</o:p></FONT></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT size=2><FONT
face="Courier New"><o:p></o:p></FONT></FONT> </P></DIV>
<DIV><FONT face="Times New Roman">Joel DeWitt<BR>Department of
Physics<BR>Oklahoma State University</FONT></DIV></BODY></HTML>