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<p class=MsoNormal>Dear all<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span lang=EN-US>Im trying to extract the interaction
energies between protein and solvent. Since PME cant be used for this, plain
cutoffs causes problems and shifted cut-offs gives incorrect energies I want to
use switched cutoff but with rather long cutoffs to get the correct energy. <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>Unfortunately my system is unstable and
within a few ps the total energy and kinetic energy fluctuates several hundred
per cent. I´ve tried different options but can´t get it to stabilize except if
I´m using any other coulomb type. Any ideas?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><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"'>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 =
20000000<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 =
20000000<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 =
20000000<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"'>nstfout =
5000<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 =
500<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 =
500<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 =
polar hydrophobic peptide SOL <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"'>nstlist = 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"'>ns_type =
grid<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 =
switch<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_switch =
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"'>rcoulomb =
1.7<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"'>rlist =
2.0<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"'>vdwtype =
switch<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_switch =
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"'>rvdw =
1.7<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
Non-Protein<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<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 =
298 298<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 style='text-autospace:none'><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 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"'>;disre_fc =
30<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 style='font-size:10.0pt;
font-family:"Courier New"'>gen_vel = yes<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>gen_temp = 298<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>gen_seed = 173529<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>unconstrained_start
= no<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal>Thanks<o:p></o:p></p>
<p class=MsoNormal>Matteus <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:12.0pt;font-family:"Times New Roman","serif"'>--------------------------------------------------------- <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Matteus
Lindgren, graduate student<br>
Department of Chemistry, Umeċ University <br>
SE-901 87 Umeċ, Sweden<br>
Phone: +46 (0)90-7865368 <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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