<DIV>Hi, David, </DIV>
<DIV>I could not understand why I can ONLY have 1 particle per cubic length unit, not<BR>more?</DIV>
<DIV>Thanks!</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 Tue, 2003-11-04 at 02:16, Albert Sun wrote:<BR>> Dear Paul.<BR>> <BR>> 'Randomly produced' meas the coordinates of atoms in x, y, z direction<BR>> are randomly distributed within a cubic box. For example, I generated<BR>> 100 or 10000 atoms randomly distributed in a box with a length of 2<BR>> nm.<BR><BR>the problem is that you can have 1 particle per cubic length unit, not<BR>more. For argon you have dimensionless units (manual ch. 2). <BR><BR>> <BR>> My intention is to use L-J particles for simulating a structure with a<BR>> large number of atoms or grains, which randomly distributed in a box.<BR>> <BR>> But I met problem and my. gro file does not work. I Checked David's<BR>> files, mdrun is OK. I don't know what is the problem in my .gro file?<BR>> <BR>> Many thanks for your time.<BR>> <BR>> Albert <BR>> <BR>> <BR>> Paul
van Maaren <MAAREN@HOME.NL>wrote:<BR>> On Mon, 3 Nov 2003, Albert Sun wrote:<BR>> <BR>> > This .gro file is obtained after EM (energy minimization)<BR>> from a randomly produced .gro file. It did not work when<BR>> mdrun.<BR>> <BR>> What do you mean with randomly produced? Maybe you should<BR>> start from the <BR>> file David send you. If you want 100 atoms, just cut out 25<BR>> and run mdrun. <BR>> That should work. Works for me at least...<BR>> <BR>> -- <BR>> Groeten,<BR>> <BR>> Paul<BR>> <BR>> <BR>> ______________________________________________________________________<BR>> Do you Yahoo!?<BR>> The New Yahoo! Shopping - with improved product search<BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,<BR>Dept. of Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala,
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