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<a class="moz-txt-link-abbreviated" href="mailto:zengyq@graduate.org">zengyq@graduate.org</a> skrev 2011-03-22 10.22:
<blockquote
cite="mid:8CDB689DBE53F51-1594-4179@web-mmc-m04.sysops.aol.com"
type="cite"><font color="black" face="arial" size="2"><br>
when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr
-o pr.trr -c b4md.pdb -g pr.log -e pr.edr &
<div>the process can not run,and there is a problem
that t = 0.000
ps: Water molecule starting at atom 90777 can not be settled.</div>
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates.
<div>i have made the dt =0.001and nsteps=10000 in the em.mdp
,but the order (szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o
pr.trr -c b4md.pdb -g pr.log -e pr.edr & ) still can not
run .how to slove this problem ?</div>
</font>
</blockquote>
Changing timestep won't help. Your simulation crashes at t=0.0,
which means your system isn't properly equillibrated, or there are
errors in the topology.<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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