<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>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><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 <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 9:31 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] pressure coupling<br> </font> <br>
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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>
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