<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>Carla<br><br><div class="gmail_quote">
On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@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;">
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>
<div><div></div><div class="h5"><br>
On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>> wrote:<br>
> Hi,<br>
> I have a problem with water molecules in my system: I'm using 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 settled.<br>
> Check for bad contacts and/or reduce the timestep.Wrote pdb files 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 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> but access is denied.<br>
><br>
> Please does anyone have a solution to propose?<br>
><br>
> Thanks<br>
> Carla<br>
><br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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