I finally figured it out. I went through every parameter step by step and it turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs would have given me a warning (hint hint). That explains why my P.E. was 10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most obvious mistake takes some time to figure out.<div>
<br></div><div>Cheers,<br><div><br></div><div>Ilya</div><div><br><div><br><div class="gmail_quote">On Fri, Apr 10, 2009 at 8:05 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Alright, sorry that I wasn't able to help. I'm confused by some apparent contradictions in your posts and I'm not sure that I'm going to be useful to you here.<br>
<br>
Quoting <a href="http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html</a>: "No matter how much minimization I do the volume of the box expands when run it using berendsen pressure coupling with a tau_p -f .1."<br>
<br>
Quoting <a href="http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html</a>: "So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization ..."<br>
<br>
Good luck.<br>
Chris.<br>
<br>
-- original message --<br>
<br>
<br>
Nope not an A/nm problem.<br>
As a simple test I take spc.gro from share/top.<br>
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o<br>
water_center.<br>
<br>
I then solvate with genbox, minimize and run using the mdp file I provided<br>
earlier.<br>
<br>
No matter how much minimization I do the volume of the box expands when run<br>
it using berendsen pressure coupling with a tau_p -f .1.<br>
<br>
Ilya<br>
<br>
<br>
On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>>wrote:<br>
<br>
[Hide Quoted Text]<br>
So your problem with the small water box was solved simply by adding more<br>
minimization? I then suspect that all of your problems are simply related to<br>
a bad starting structure -- and by the sound of it is really is very bad.<br>
Are you sure that you don't have an angstrom / nm problem here?<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
So I got my small water box (800 waters) to behave stably with pressure<br>
coupling after more minimization but I still can't get my large system to<br>
work with pressure coupling. I tried minimizing but I can never get the<br>
Fmax to be less 102, which is pretty normal for protein/water simulations of<br>
large proteins, at least from my experience. I have since run 400 ps NVT<br>
as ...<br>
<br>
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</blockquote></div><br></div></div></div>