Nope not an A/nm problem. <div><br></div><div>As a simple test I take spc.gro from share/top.<div><br></div><div>I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o water_center.</div><div><br></div><div>
I then solvate with genbox, minimize and run using the mdp file I provided earlier. </div><div><br></div><div>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.</div>
<div><br></div><div>Ilya</div><div><br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale <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;">So your problem with the small water box was solved simply by adding more minimization? I then suspect that all of your problems are simply related to a bad starting structure -- and by the sound of it is really is very bad. 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 Fmax<br>
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 as<br>
the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am<br>
using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure<br>
what else to do except run NVT, which is what I was going to do after I got<br>
the density equilibrated. BTW, I am using octahedral PBC, but that should<br>
not make a difference with respect to P coupling, should it? Below is my<br>
whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in<br>
10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the<br>
amount of time it takes for my system to expand increases but it still<br>
expands.<br>
<br>
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</blockquote></div><br></div></div>