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Hi,<br><br>Never ever use switched cut-off's!<br>Switched cut-off's can give extremely strong artifacts.<br>In 4.1 grompp will warn you about this.<br><br>Switch gives you correct energies at short range, but incorrect forces<br>in the switching region.<br>What you want is correct forces up to (nearly) the cut-off.<br>Shift does this.<br>But reaction-field does this smoother and it even has a physical interpretation.<br>So use RF if you can not use PME.<br><br>But why can't you use PME, you have pbc, right?<br><br>Berk<br><br><br><hr id="stopSpelling">From: matteus.lindgren@chem.umu.se<br>To: gmx-users@gromacs.org<br>Date: Fri, 7 Aug 2009 13:13:24 +0200<br>Subject: [gmx-users] System instability with switched cut-off<br><br>
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<p class="EC_MsoNormal">Dear all</p>
<p class="EC_MsoNormal"> </p>
<p class="EC_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. </span></p>
<p class="EC_MsoNormal"><span lang="EN-US"> </span></p>
<p class="EC_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?</span></p>
<p class="EC_MsoNormal"><span lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">title =
Dyna</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">cpp =
/usr/bin/cpp</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">constraints =
hbonds</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">integrator =
md</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">dt =
0.002</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nsteps =
20000000</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstxout =
20000000</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstvout =
20000000</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstfout =
5000</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstlog =
250</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstenergy =
500</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstxtcout =
500</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">xtc_grps = </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">energygrps =
polar hydrophobic peptide SOL </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">nstlist = 1</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">ns_type =
grid</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">coulombtype =
switch</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">rcoulomb_switch =
1.4</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">rcoulomb =
1.7</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">rlist =
2.0</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">vdwtype =
switch</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">rvdw_switch =
1.4</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">rvdw =
1.7</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">tcoupl =
nose-hoover</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">tc-grps = Protein
Non-Protein</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">tau_t =
0.5 0.5</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">ref_t =
298 298</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">Pcoupl =
parrinello-rahman</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">tau_p =
1.0</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">compressibility =
4.5e-5</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">ref_p =
1.0</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US">;disre_fc =
30</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';">gen_vel = yes</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';">gen_temp = 298</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; font-family: 'Courier New';">gen_seed = 173529</span></p>
<p class="EC_MsoNormal"><span style="font-size: 10pt; font-family: 'Courier New';">unconstrained_start
= no</span></p>
<p class="EC_MsoNormal"><span style="font-size: 10pt;"> </span></p>
<p class="EC_MsoNormal">Thanks</p>
<p class="EC_MsoNormal">Matteus <span lang="EN-US"></span></p>
<p class="EC_MsoNormal"><span lang="EN-US"> </span></p>
<p class="EC_MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman','serif';" lang="EN-US">--------------------------------------------------------- </span></p>
<p class="EC_MsoNormal"><span style="font-size: 10pt; font-family: 'Arial','sans-serif';" lang="EN-US">Matteus
Lindgren, graduate student<br>
Department of Chemistry, Umeå University <br>
SE-901 87 Umeå, Sweden<br>
Phone: +46 (0)90-7865368 </span></p>
<p class="EC_MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman','serif';" lang="EN-US"> </span></p>
<p class="EC_MsoNormal"><span lang="EN-US"> </span></p>
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