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<div class=Section1 dir=RTL>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Greetings
dear Gromacs users,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>I
have recently been simulating a POPG membrane* in water (SPC). Several of my
simulations after running well into the 10ns and 20ns are sometimes getting a
"Forces for atom X are large". <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>I'm
rather unsure as to the cause of this situation. Moreover, as far as I can tell
from viewing the simulation, the system <u>does NOT</u> explode (as may be
suggested by wiki.gromacs and some previous answers to this kind of situation).
The rest of the simulation looks much as it did in the beginning.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>I
would be interested (and thankful!) to hear any of your opinions as to why I'm
getting this message (or how to catch the culprit), and more importantly, how
to prevent it from happening in the future. <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>The
following below includes the error message as well as my md.mdp settings.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Lipid
membrane (64 L and 64 D popg molecules) are coupled together, also solvent is
coupled together with ions. Pressure is semiisotropic.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Thanks
a lot, <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Shay.
<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Beginning
of Warning message (the atom in reference is C4 of L-POPG molecule).<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>---------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>Reading
frame 600 time 6000.000 Warning at frame 693.
Forces for atom 3820 are large (-10016.3)</span></font></b><b><font size=1
face="Courier New"><span lang=HE dir=RTL style='font-size:8.0pt;font-family:
"Courier New";font-weight:bold'><o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>Last
frame 1000 time 10000.000<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>---------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>md.mdp
settings<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>---------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>title
= Full MD<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>cpp
= /usr/bin/cpp<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>constraints
= all-bonds<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>integrator
= md<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>dt
= 0.002 ; ps</span></font></b><span dir=RTL></span><b><font
size=1 face="Courier New"><span lang=HE dir=RTL style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'><span dir=RTL></span> !</span></font></b><b><font
size=1 face="Courier New"><span style='font-size:8.0pt;font-family:"Courier New";
font-weight:bold'><o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>nsteps
= 5000000 ; 10000 ps run<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>nstxout
= 5000<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>nstvout
= 5000<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>nstfout
= 5000<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>pbc
= xyz<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>nstlist
= 10<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>ns_type
= grid<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>rlist
= 1.2<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>coulombtype
= PME<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>rcoulomb
= 1.2<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>vdw-type
= Cut-off<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>rvdw
= 1.2<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>gen_vel
= no<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>fourierspacing
= 0.1<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>fourier_nx
= 0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>fourier_ny
= 0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>fourier_nz
= 0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>pme_order
= 4<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><span dir=RTL></span><b><font size=1 face="Courier New"><span lang=HE
dir=RTL style='font-size:8.0pt;font-family:"Courier New";font-weight:bold'><span
dir=RTL></span>; </span></font></b><b><font size=1 face="Courier New"><span
style='font-size:8.0pt;font-family:"Courier New";font-weight:bold'>Berendsen
temperature coupling is on in two groups<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>Tcoupl
= berendsen<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>tau_t
= 0.1 0.1<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>tc-grps
= sol_ions popg_membrane_DL<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>ref_t
= 310 310<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><span dir=RTL></span><b><font size=1 face="Courier New"><span lang=HE
dir=RTL style='font-size:8.0pt;font-family:"Courier New";font-weight:bold'><span
dir=RTL></span>; </span></font></b><b><font size=1 face="Courier New"><span
style='font-size:8.0pt;font-family:"Courier New";font-weight:bold'>Pressure
coupling is on<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>Pcoupl
= berendsen<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>pcoupltype
= semiisotropic<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>tau_p
= 1.0 1.0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>compressibility
= 4.5e-5 0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=1 face="Courier New"><span style='font-size:8.0pt;
font-family:"Courier New";font-weight:bold'>ref_p
= 1.0 1.0<o:p></o:p></span></font></b></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>---------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=1 face=Arial><span style='font-size:8.0pt;font-family:Arial'>*
POPG membrane refers to the following article </span></font><font face=Arial><span
style='font-family:Arial'>(</span></font><font size=1 face=AdvP6EC5><span
style='font-size:8.0pt;font-family:AdvP6EC5'>Atomic-Scale Structure and
Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers
with Na</span></font><font size=1 face=AdvPS7DED><span style='font-size:8.0pt;
font-family:AdvPS7DED'>1 </span></font><font size=1 face=AdvP6EC5><span
style='font-size:8.0pt;font-family:AdvP6EC5'>Counterions, </span></font><font
size=1 face=AdvP6EC0><span style='font-size:8.0pt;font-family:AdvP6EC0'>Biophysical
Journal Volume 92 February 2007 1114</span></font><font size=1><span
style='font-size:8.0pt'>–</span></font><font size=1 face=AdvP6EC0><span
style='font-size:8.0pt;font-family:AdvP6EC0'>1124 </span></font><font
face=AdvP6EC0><span style='font-family:AdvP6EC0'>)</span></font><font
face=Arial><span style='font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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