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<DIV>Hi, David and users,</DIV>
<DIV>My simple case study has not shown good results, the 9atom always explod, even though I tried many times to adjuster various parameters.</DIV>
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<DIV>Greatly appreciate if you could help me to have a look on these files and find out where is the problem? the following commnets are used: </DIV>
<DIV><FONT size=2>
<P>grompp -v -f em.mdp -c 9atom.gro -o em.tpr -p 9atom.top</P></FONT></DIV>
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<P>mdrun -v -s em -o em -c afterem</P>
<P>grompp -f 9atom.mdp -o s1 -c afterem.gro -p 9atom.top -n atom.ndx</P>
<P>mdrun -s s1.tpr -o s1.trr -c s1.gro -pi pull.ppa -pn atom.ndx</P></FONT></DIV>
<DIV>(I attached three files here, three more files are attached in another mail)</DIV>
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<DIV>Thanks!</DIV>
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<DIV>Albert</DIV>
<DIV><BR><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 Fri, 2003-08-29 at 18:17, Albert Sun wrote:<BR>> Hi, David, <BR>> Do you know what is the reason that atoms explod? <BR>> Is it because that I did not include bond force and constraints or<BR>> other wrong parameters?<BR>Anything, charged atoms with no van der waals or something like that.<BR>Something in your topology. If you give all atoms zero charge and a<BR>reasonable vanderwaals params it will work fine.<BR>> <BR>> thanks!<BR>> <BR>> <BR>> <BR>> <BR>> David <SPOEL@XRAY.BMC.UU.SE>wrote: <BR>> On Thu, 2003-08-28 at 23:07, Albert Sun wrote:<BR>> > Dear David van der Spoel,<BR>> > I am testing a simple case, and prepared top and gro<BR>> files as<BR>> > attached, when I ran EM.mdp and 9atom.mdp, and see<BR>> ngmx, it has the<BR>> > error: segmentation fault.<BR>> > (em.mdp file is attached in another
email)<BR>> > Could you help me to have a look?<BR>> <BR>> I see a system of 9 atoms in a plane which explodes<BR>> after roughly 100 fs<BR>> (I decreased nstxout to 5 to see it).<BR>> <BR>> If you do not see that, then I suggest you try to run<BR>> it on a Linux or<BR>> Unix box first. By the way, ngmx won't work on a DOS<BR>> anyway.<BR>> <BR>> <BR>> -- <BR>> Groeten, David.<BR>> ________________________________________________________________________<BR>> Dr. David van der Spoel, Dept. of Cell and Molecular<BR>> Biology<BR>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>> phone: 46 18 471 4205 fax: 46 18 511 755<BR></BLOCKQUOTE></DIV></DIV></DIV></DIV></DIV><p><hr SIZE=1>
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