<DIV>
<DIV>Dear David and Gmx-users,</DIV>
<DIV>I have a few stupid questions:</DIV>
<DIV>How to simulate simple Lennard Jones particles in Gromacs? </DIV>
<DIV>In .top file, we don't need input bond and angle data, is it right?</DIV>
<DIV>How to specify force field in .top file?</DIV>
<DIV> </DIV>
<DIV>Greatly appreciate your clarification.</DIV>
<DIV> </DIV>
<DIV>Thanks </DIV>
<DIV> </DIV>
<DIV>Albert</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><BR><B><I>Albert Sun <albert_sun9@yahoo.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">
<DIV>Dear Groeten, David</DIV>
<DIV>How to start simple Lennard Jones particles in Gromacs?</DIV>
<DIV>by specify force field: ffgmx</DIV>
<DIV><BR>thanks!</DIV>
<DIV> </DIV>
<DIV>Albert</DIV>
<DIV> </DIV>
<DIV><BR><B><I>David <spoel@xray.bmc.uu.se></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">On Sat, 2003-09-20 at 21:09, Albert Sun wrote:<BR>> Hi, Dear Anton,<BR>> Atoms exploded problem still remains, when I view .trr file by VMD,<BR>> all atoms suddenly disappear.<BR>> I tried ngmx, it had error: float exception. <BR>> I tried trjconv -dump, it showed warning: "no output, trajectory ended<BR>> at 3" <BR>> <BR>> could you give me more hints ? <BR><BR><BR>It seems to me that you have just a weird system with all atoms placed<BR>in a plane, and large forces between them.<BR><BR>If you intend to simulate some sort of two dimensional crystal, you<BR>should probably start with simple Lennard Jones particles.<BR>-- <BR>Groeten, David.<BR>________________________________________________________________________<BR>Dr. David van der Spoel, Dept. of Cell and Molecular Biology<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18
511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE>
<P>
<HR SIZE=1>
Do you Yahoo!?<BR><A href="http://us.rd.yahoo.com/evt=10469/*http://sitebuilder.yahoo.com">Yahoo! SiteBuilder</A> - Free, easy-to-use web site design software</BLOCKQUOTE></DIV><p><hr SIZE=1>
Do you Yahoo!?<br>
<a href="http://us.rd.yahoo.com/evt=10469/*http://sitebuilder.yahoo.com">Yahoo! SiteBuilder</a> - Free, easy-to-use web site design software