This is the mdp file i use for my energy minimization<br><br>Thanks<br>Carla<br>;<br>; 1W5B all-atom<br>; Input file<br>;<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = none <br>
integrator = steep<br>nsteps = 500 <br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000.0<br>emstep = 0.01 <br><br>nstcomm = 1<br>ns_type = grid<br>
nstlist = 10<br>nstxout = 1<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>
pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br><div class="gmail_quote">On Fri, Oct 2, 2009 at 12:46 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">jochen@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
when I get the error message: "water molecule cannot be settled",does it have to do with the SETTLE parameter in gromacs?<br>
If yes, does anyone know how to fix this?<br>
</blockquote></div>
No, that probably means that you have clashes (atomic overlaps) in your system which cause huge forces. Track down which atoms cause the error message and remove the clashes.<br>
<br>
If that error message appeares during energy minimization, using flexible water may help. Define -DFLEXIBLE in the mdp file, and check in the spc/itp4p/tip3p.itp file if flexible water molecules are actually defined.<br>
<br>
Good luck,<br>
Jochen<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Carla<div class="im"><br>
<br>
On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Carla Jamous wrote:<br>
<br>
Hi,<br>
I have a problem, I'm running EM, it works but when it comes<br>
to doing position-restrained MD, it gives me this error message:<br>
<br>
Segmentation fault<br>
Large VCM(group System): -1293135642624.00000,<br>
358859374592.00000, -846768177152.00000, T-cm: 6.13428e+26<br>
<br>
I searched the archives, it says to check-out:<br>
<a href="http://oldwiki.gromacs.org" target="_blank">oldwiki.gromacs.org</a> <<a href="http://oldwiki.gromacs.org" target="_blank">http://oldwiki.gromacs.org</a>><br>
<<a href="http://oldwiki.gromacs.org" target="_blank">http://oldwiki.gromacs.org</a>><br>
<br>
but this site doesn't exist anymore.<br>
<br>
<br>
All of the content has been moved to the new site, albeit a very<br>
different organization system. You should still be able to find<br>
it with a bit of digging.<br>
<br>
<br>
So please can anyone give me the answer to this problem?<br>
<br>
<br>
The problem is that your system is suddenly moving very fast,<br>
probably blowing up. Without a further description of the system<br>
and seeing your .mdp file, it's hard to say what the root problem is.<br>
<br>
-Justin<br>
<br>
<br>
Cheers,<br>
Carla<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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</div></blockquote><font color="#888888">
<br>
<br>
-- <br>
---------------------------------------------------<br>
Dr. Jochen Hub<br>
Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4714451 Fax: +46-18-511755</font><div><div></div><div class="h5"><br>
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