<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 18/08/2011 10:14 AM, Itamar Kass wrote:
<blockquote
cite="mid:AF3C5B81-E229-4ED9-A0FD-907C147DB00F@monash.edu"
type="cite">Hi Chris and Justin,
<div><br>
</div>
<div>
<div>
<div>On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div><br>
<br>
<a moz-do-not-send="true"
href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>
wrote:<br>
<blockquote type="cite">You'll need to provide a much
better report than this if you want to receive any
useful help.<br>
</blockquote>
<blockquote type="cite">Copy and paste the exact commands
of what you did<br>
</blockquote>
<blockquote type="cite">Copy and paste the exact log file
and error messages<br>
</blockquote>
<br>
</div>
</blockquote>
<div><br>
</div>
<div>The command I had used (for both 4.0.7 and 4.5.4) are:</div>
<div><br>
</div>
<div><font class="Apple-style-span" face="'Courier New'">pdb2gmx
-f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i
1EXR.itp<br>
editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic<br>
<br>
genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p
1EXR.top -seed 5<br>
<br>
grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr<br>
genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top
-pname NA+ -nname CL- -np 17 -seed 66</font></div>
<div><font class="Apple-style-span" face="'Courier New'"><br>
</font></div>
<div><font class="Apple-style-span" face="'Courier New'">grompp
-f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr<br>
<br>
mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e
1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro<br>
<br>
grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr<br>
<br>
mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x
1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr
-c 1EXR_pr.gro<br>
<br>
grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o
md.tpr<br>
<br>
mpirun mdrun_d_mpi -v -stepout 10000 -s md.tpr -x
1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr
-c 1EXR_md.gro </font><br>
</div>
</div>
</div>
</blockquote>
<br>
So you're doing solvated EM, then position-restrained NPT MD, then
NPT. Sounds to me like you might have a bad initial contact that
can't relax under solvated EM, nor under PR-NPT, and is getting
numerically lucky in 4.0.7 and not under 4.5.4. If so, then careful
inspection of the start of the 4.0.7 run might show this. Vacuo EM
of the solute might help if the problem is intra-solute. Have you
explored the suggestions here? <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
Mark<br>
</body>
</html>