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<DIV><FONT face=Verdana color=#000000 size=2>I guess you have not listed all the
dihedrals in the configuration of a ethanol molecule.</FONT></DIV>
<DIV><FONT face=Verdana size=2>In your .top file, there are only
two dihedrals, you might need to include all others.</FONT></DIV>
<DIV><FONT face=Verdana size=2>By the way, check the other part of your topology
to avoid other incorrect inputs.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Verdana size=2>Best regards.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Verdana size=2>Yue Shao</FONT> </DIV>
<DIV><FONT face=Verdana color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV align=left>
<DIV align=left><FONT face=Verdana size=2>
<HR style="WIDTH: 122px; HEIGHT: 2px" SIZE=2>
</FONT></DIV>
<DIV><FONT color=#c0c0c0><FONT face=Verdana size=2>silvester.thu</FONT></DIV>
<DIV><FONT face=Verdana size=2>2008-05-14</FONT></FONT></DIV></DIV>
<DIV><FONT face=Verdana size=2>
<HR>
</FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG> Jussi
Lehtola</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-05-14 11:28:31</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>收件人：</STRONG> Discussion list for
GROMACS users</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>抄送：</STRONG> </FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>主题：</STRONG> RE: [gmx-users] Energy
minimisation problem</FONT></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>
<DIV> </DIV>
<DIV>On Tue, 2008-05-13 at 20:32 +0300,
Jussi Lehtola wrote:</DIV>
<DIV>> On Tue, 2008-05-13 at 14:34 +0100,
Kukol, Andreas wrote:</DIV>
<DIV>> > First try the EM/MD of
1 molecule in vacuum ('ethanol-gas') and
check, if it looks reasonable.</DIV>
<DIV>> > </DIV>
<DIV>> Thanks, using the vacuum method I
seem to get better results.</DIV>
<DIV> </DIV>
<DIV>It seems I spoke too soon. Energy
minimising the one-particle structure</DIV>
<DIV>in vacuum gives me the following
potential energies:</DIV>
<DIV> </DIV>
<DIV>methanol 21.4</DIV>
<DIV>ethanol 9.4</DIV>
<DIV>propanol 3.8</DIV>
<DIV>butanol 4.1</DIV>
<DIV>pentanol 12.2</DIV>
<DIV>hexanol 81.0</DIV>
<DIV> </DIV>
<DIV>All minimizations have converged with Fmax
< 1e-3. Are these energies</DIV>
<DIV>reasonable? The energies of methanol and
hexanol are somewhat high.</DIV>
<DIV> </DIV>
<DIV>Energy minimisation with a system of
4913 methanol molecules with</DIV>
<DIV>initial density of 500 kg/m^3 and
periodic boundary conditions gives as</DIV>
<DIV>potential energy Epot = -1.67e5, however
the forces do not converge. </DIV>
<DIV>Running the system with Berendsen pressure
and temperature thermostats</DIV>
<DIV>(p = 1 bar, T = 300 K)
results in a crash after 82 ps.
The total energy</DIV>
<DIV>is positive and of the order 1e5.</DIV>
<DIV>-- </DIV>
<DIV>------------------------------------------------------</DIV>
<DIV>Jussi Lehtola, FM, Tohtorikoulutettava</DIV>
<DIV>Fysiikan laitos, Helsingin Yliopisto</DIV>
<DIV>jussi.lehtola@helsinki.fi, p. 191 50673</DIV>
<DIV>------------------------------------------------------</DIV>
<DIV>Mr. Jussi Lehtola, M. Sc., Doctoral
Student</DIV>
<DIV>Department of Physics, University of
Helsinki, Finland</DIV>
<DIV>jussi.lehtola@helsinki.fi</DIV>
<DIV>------------------------------------------------------</DIV>
<DIV> </DIV>
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