<div>Hi, Gromacs users, </div>
<div> </div>
<div>I was caught by a big problem with molecular dynamic investigation of an cyclic peptide nanotube. When i do energy minimization with em.mdp parameter file as follows, it gave out a warning: <span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">Warning: 1-4 interaction between 135 and 144 at distance larger than 1 nm. <font color="#000000">I ignored it and went on the next step with pr.mdp as follows, but it crashed with the following information:</font></font></span></div>
<div><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </div>
<div><span lang="EN-US" style="COLOR: blue">
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">Wrote pdb files with previous and current coordinates</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] *** Process received signal ***</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] Signal: Segmentation fault (11)</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] Signal code: Address not mapped (1)</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] Failing at address: 0xba8e28</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] [ 9] mdrun_ompi [0x412e8a]</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">[node1:15777] *** End of error message ***</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman">Segmentation fault</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000">I am extremely puzzed and don't know how to solve this problem. In additon, m<span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"><font color="#000000">y previous system runs normally with the same parameter file. </font></span></span></font></span></p>
</span>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000">##############em.mdp file</font></span></p><span lang="EN-US" style="COLOR: blue">
<p>cpp = /lib/cpp<br>define = -DPOSRES<br>constraints = none<br>integrator = steep<br>nsteps = 100<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 2000<br>
emstep = 0.01</p>
<p>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>rcoulomb = 1.0<br>rvdw = 1.0<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>
</p></span>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000">#########pr.mdp</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue">title = Yo<br>cpp = /lib/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 2500 ; total 5 ps.<br>nstcomm = 1<br>nstxout = 500<br>nstvout = 1000<br>nstfout = 0<br>
nstlog = 500<br>nstenergy = 500<br>nstlist = 5<br>ns_type = grid<br>coulombtype = PME<br>rlist = 0.9<br>rcoulomb = 0.9<br>rvdw = 0.9<br>
fourierspacing = 0.12<br>pme_order = 4<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein<br>tau_t = 0.1<br>
ref_t = 10<br>; Energy monitoring<br>energygrps = Protein<br>; Pressure coupling is not on<br>Pcoupl = berendsen<br>pcoupltype = anisotropic<br>tau_p = 1<br>
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<br>ref_p = 1 1 1 1 1 1<br>; Generate velocites is on at 300 K.<br>gen_vel = no</span><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"><br>
gen_temp = 300.0<br>gen_seed = 173529<br></span></span><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"></span></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"></span></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"><font color="#000000">Look forward to your help. Thanks in advance.</font></span></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"></span></span> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><span lang="EN-US" style="COLOR: blue"><font color="#000000">Huifang</font> </span></span></p></div>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: blue"><font face="Times New Roman" color="#000000"></font></span> </p>