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<DIV><FONT face=Calibri>I don't know the conditions you use with your system,
but sometimes there are problems when you use pressure coupling in a system with
positionally restrained or fixed atoms.</FONT></DIV>
<DIV><FONT face=Calibri>Cheers.</FONT></DIV>
<DIV><FONT face=Calibri> Lucio.</FONT></DIV>
<DIV style="FONT: 10pt Tahoma">
<DIV><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=ilchorny@gmail.com
href="mailto:ilchorny@gmail.com">Joe Joe</A> </DIV>
<DIV><B>Sent:</B> Friday, April 10, 2009 12:12 PM</DIV>
<DIV><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A> </DIV>
<DIV><B>Subject:</B> Re: [gmx-users] Pressure Coupling Problem</DIV></DIV></DIV>
<DIV><BR></DIV>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
title="mailto:chris.neale@utoronto.ca CTRL + clic para seguir el vínculo"
href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</A>></SPAN>
wrote:<BR>
<BLOCKQUOTE
style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex"
class=gmail_quote>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
title="http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html CTRL + clic para seguir el vínculo"
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>_______________________________________________<BR>gmx-users
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