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<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>Hi all!<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>I am quite new to Gromacs
and am wondering why I can´t see any box fluctuations during a NPT run of
protein + urea solvent in dodecahedron. In the energy output file I can see
that the Box-X,Y,Z values only fluctuate <1%. <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>However the pressure average
is reasonably close to the ref_p value, 1.7 instead of 1.0 during 20ns. Should
there not be any box fluctuations with the parrinello-rahman algorithm? <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>I use the input settings
specified below.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>title =
Dyna<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>cpp =
/usr/bin/cpp<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>constraints =
hbonds<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>constraint_algorithm =
lincs<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>lincs_iter = 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>integrator =
md<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>dt =
0.002<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nsteps =
8000000<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nstxout =
4000000<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nstvout =
3000<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nstlog =
250<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nstenergy =
250<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>nstxtcout =
250<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>xtc_grps = <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>energygrps =
Protein SOL UREA CL-<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>nstlist = 5<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>ns_type = grid<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rlist = 1.1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>coulombtype =
PME<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>rcoulomb =
1.1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>rvdw =
1.4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>fourierspacing =
0.14<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>pme_order = 6<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>optimize_fft =
yes<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>tcoupl =
nose-hoover<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>tc-grps =
Protein SOL UREA CL-<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>tau_t =
0.5 0.5 0.5 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>ref_t =
308 308 308 308<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>Pcoupl =
parrinello-rahman<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>tau_p =
1.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New"'>compressibility =
4.5e-5<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>ref_p
= 1.0<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>Thank
you!<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>Regards</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Matteus
Lindgren <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Graduate
student <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Department
of Chemistry<br>
Umeċ University<br>
SE-901 87 Umeċ, Sweden<br>
Tel: +46 (0)90 786 53 68<br>
e-mail: <a href="mailto:barbara.addario@chem.umu.se"><span style='color:blue'>matteus.lindgren@chem.umu.se</span></a></span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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