<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Mark,<div><br></div><div>We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD.</div><div><br></div><div>Itamar.</div><div> <br><div><div>On 18/08/2011, at 10:31 AM, Mark Abraham wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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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>
</div>
-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<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.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">-----<br>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br><br>===========================================<br>| Itamar Kass, Ph.D.<br>| Postdoctoral Research Fellow<br>|<br>| Department of Biochemistry and Molecular Biology<br>| Building 77 Clayton Campus<br>| Wellington Road<br>| Monash University,<br>| Victoria 3800<br>| Australia<br>|<br>| Tel: +61 3 9902 9376<br>| Fax: +61 3 9902 9500<br>| E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>============================================<br></span>
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