<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Thank you very much.</span></div><div><span><br></span></div><div><span>Yes, I checked NPT run and I saw the size and volume of box had been increased. So I increased size of box to 12.</span></div><div><span>My system consists of: 151 lipids+151 ions+16200 water and antifreezawater molecules<br></span></div><div>May I know your idea about this, please?</div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Sara<br></span></div><div><br></div> <div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, December 17, 2011 10:22 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] pressure coupling<br> </font> <br>
<div id="yiv677208950">
<div>
On 17/12/2011 5:40 PM, mohammad agha wrote:
<blockquote type="cite">
<div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:verdana, helvetica, sans-serif;
font-size:12pt;">
<div><span>Thank you very much.</span></div>
<div><span>Excuse me, I did another thing, may I know is it
right, Please?<br>
</span></div>
<div>I did editconf before equilibration (pr.mdp) and increased
my box vector from 11.2 to 12:</div>
<div>editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12
12 12 -center 6 6 6<br>
and I minimized my system (out.gro) and then did equilibration
(pr.mdp). My system gave me warning for box sizes 11.4, 11.6
and 11.8, consequently I select 12 and pr.mdp is run without
warning.</div>
<div>Is it right?</div>
</div>
</blockquote>
<br>
We don't know. You've been changing your box volume but haven't said
anything about the contents. You need to look at how the box changes
over the NPT run, like I said last time. If your generated solvent
density was wrong such that you needed to add about 20% more volume,
then expect to need to equilibrate for quite a while.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:verdana, helvetica, sans-serif;font-size:12pt;">
<div><br>
</div>
<div>Best Regards</div>
<div>Sara<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div style="font-family:verdana, helvetica, sans-serif;font-size:12pt;">
<div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a rel="nofollow" class="yiv677208950moz-txt-link-rfc2396E" ymailto="mailto:Mark.Abraham@anu.edu.au" target="_blank" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight:bold;">To:</span></b>
Discussion list for GROMACS users
<a rel="nofollow" class="yiv677208950moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight:bold;">Sent:</span></b>
Saturday, December 17, 2011 9:31 AM<br>
<b><span style="font-weight:bold;">Subject:</span></b>
Re: [gmx-users] pressure coupling<br>
</font> <br>
<div id="yiv677208950">
<div> On 17/12/2011 4:58 PM, mohammad agha wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:verdana, helvetica, sans-serif;font-size:12pt;">
<div>Dear GROMACS Users</div>
<div><br>
</div>
<div>I have a warning after doing pr.mdp as
followed, I read errors in GROMACS site and
checked mailing list, but my warning is only step1
and after that equilibration is run normally till
end. <br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>5000000 steps, 150000.0 ps.<br>
step 0<br>
Step 1 Warning: pressure scaling more than 1%,
mu: 1.04679 1.04679 1.04679<br>
<br>
Step 1 Warning: pressure scaling more than 1%,
mu: 1.04679 1.04679 1.04679<br>
</div>
<div><br>
</div>
<div>my pr.mdp about pressure coupling is:</div>
<div><br>
</div>
<div>pcoupl = berendsen<br>
pcoupltype = isotropic ; uniform scaling of
box vectors<br>
tau_p = 4 ; time constant, in ps<br>
ref_p = 1.0 ; reference pressure, in
bar<br>
compressibility = 4.5e-5 ;isothermal
compressibility of water, bar^-1</div>
<div><br>
</div>
<div><br>
</div>
<div>I work in Martini Coarse-Grained and my time
step is 0.03 ps. I increased tau_p but my warning
increased to step 1 and step 11, I think this
warning since it is only in initial steps isn't
important, is my idea right?</div>
<br>
</div>
</blockquote>
<br>
That kind of thing is normal in the very early stages of
NPT equilibration when the volume is not quite right.
mdrun is just warning you that there are some changes
going on. Use g_energy to see those. If it bothers you,
then you will want to adjust your density (i.e. number
of water molecules) before starting.<br>
<br>
Mark<br>
</div>
</div>
<br>
-- <br>
gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
http://lists.gromacs.org/mailman/listinfo/gmx-users<br>
Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the <br>
www interface or send it to <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>
<br>
</div>
</div>
</div>
<br>
<fieldset class="yiv677208950mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div>
</div><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div> </div></body></html>