Hi,<br><br>another point you should consider is that the atom/molecule number in the pdb or gro file are not necessarally the what you see in your output. You should use gmxdump in such cases to trace the molecule.<br><br>
<br>Cheers,<br>Itamar<br><br>---<br><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@med.monash.edu.au">Itamar.Kass@med.monash.edu.au</a><br>============================================<br><br><div class="gmail_quote">
On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <span dir="ltr"><<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.com</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="gmail_quote">2009/9/29 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><div class="im"><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br>
<br>
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;">
<br>
Thank you for your reply,<br>
but none of the water molecules with error messages is trapped inside my protein, nor is it in contact with the protein or the ions in my system.<br>
<br></blockquote></div></blockquote></div><div><br>Also if the water molecules are positioned properly, you can try define = -DPOSRES_WATER in your .mdp file with a high value set in your topology(.top) file under [position restraint] section as,<br>
<br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 100000 100000 100000<br>#endif<br><font color="#888888"><br>
-Manik<br>
<br></font></div><div><div></div><div class="h5"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
</blockquote>
</div>
Then you need to watch the trajectory and see where things go wrong. In unstable systems, I often set "nstxout = 1" to capture as many frames in the .trr file as possible (if the crash is happening early, as it is in your case).<br>
<br>
Likely, energy minimization did not resolve all the bad contacts, but may still have converged within your criteria. You could also specify a lower target Fmax during EM to see if things resolve.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Carla<div><br>
<br>
On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a> <mailto:<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>>> wrote:<br>
<br>
Hi Carla,<br>
<br>
You may have a water molecule trapped inside your protein. Check the<br>
water molecule with the given atom number in a viewer, together with<br>
your structure. If it is inside, you can try to remove it manually<br>
from the system, editing the structure file and decreasing the amount<br>
of solvent listed in te topology file. If you edit the .gro file, do<br>
mind to decrease the number on the second line (the number of atoms)<br>
by three.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous<br></div><div>
<<a href="mailto:carlajamous@gmail.com" target="_blank">carlajamous@gmail.com</a> <mailto:<a href="mailto:carlajamous@gmail.com" target="_blank">carlajamous@gmail.com</a>>> wrote:<br>
> Hi,<br>
> I have a problem with water molecules in my system: I'm using<br>
Gromacs with<br>
> ffamber94 force-field. During minimization, I have this message:<br>
><br>
> t = 0.014 ps: Water molecule starting at atom 10045 can not be<br>
settled.<br>
> Check for bad contacts and/or reduce the timestep.Wrote pdb files<br>
with<br>
> previous and current coordinates<br>
><br>
> The minimization converged. However, molecular dynamics were stopped.<br>
> I tried minimization with different parameters: Flexible,<br>
> position-restrained, reducing my timestep, etc... and nothing worked.<br>
><br>
> I also tried one simulation with TIP3P water model and another<br>
simulation<br>
> with SPC water model and I still get the same error.<br>
> I tried to access: <a href="http://oldwiki.gromacs.org" target="_blank">oldwiki.gromacs.org</a><br></div>
<<a href="http://oldwiki.gromacs.org" target="_blank">http://oldwiki.gromacs.org</a>> but access is denied.<div><br>
><br>
> Please does anyone have a solution to propose?<br>
><br>
> Thanks<br>
> Carla<br>
><br>
> _______________________________________________<br>
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<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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