<br /><br /><span>On 06/03/11, <b class="name">Moeed </b> &lt;lecielll@googlemail.com&gt; wrote:</span><blockquote cite="mid:AANLkTikFj5F+waQvgSi6P0MqXAmPuXsQGAK1aAwN27Yr@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi everyone,<br /><br />My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything works fine till the end of run and comparison between energy terms (up until the crash point) shows very slight difference between two runs ( less than 2% even for electrostatic terms). I am aware that blowing up is due to unphysical forces but is this happening by accidient or there is an underlying reason I should take care of.</div></blockquote><br />Don't change fourierspacing unless you can measure the error so introduced (which you can't, easily, yet), and can defend the assertion that it does not affect your observations.<br /><br />Generating velocities at the start of an NPT run seems unwise. A better-behaved protocol will equilibrate the velocities under NVT before fixing the density under NPT, before then moving to the production simulation ensemble.<br /><br />Mark<br /><br /><blockquote cite="mid:AANLkTikFj5F+waQvgSi6P0MqXAmPuXsQGAK1aAwN27Yr@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Thanks,<br />Best,<br />Moeed<br /><br />========================================<br />step 164300, remaining runtime:   241 s          <br />step 164400, remaining runtime:   240 s          <br />step 164500, remaining runtime:   240 s          <br />
step 164600, remaining runtime:   239 s          <br />
Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 which is larger than the 1-4 table size 2.250 nm<br />
These are ignored for the rest of the simulation<br />This usually means your system is exploding,<br />if not, you should increase table-extension in your mdp file<br />or with user tables increase the table size<br />=========================================<br />
results till t=320 ps (before first run crash)<br />fourierspacing      =  0.12 <br /><br />

<p class="MsoNormal">LJ-14<span style="">                      
</span>757.246<span style="">    </span>26.6239<span style="">    </span>26.5661 -0.0189929<span style="">   </span>-6.07777</p>

<p class="MsoNormal">Coulomb-14<span style="">                
</span>-186.509<span style="">    </span>15.9866<span style="">    </span>15.9529 -0.0112174<span style="">    </span>-3.5896</p>

<p class="MsoNormal">LJ (SR)<span style="">                   
</span>-2691.84<span style="">    </span>117.026<span style="">    </span>107.231<span style=""> 
</span>-0.507373<span style="">   </span>-162.361</p>

<p class="MsoNormal">Coulomb (SR)<span style="">               
</span>725.662<span style="">    </span>17.6483<span style="">    </span>17.5876<span style=""> 
</span>0.0158275<span style="">    </span>5.06483</p>

<p class="MsoNormal"> </p><p class="MsoNormal">fourierspacing      =  0.3</p><p class="MsoNormal"><br /></p>

<p class="MsoNormal">LJ-14<span style="">                      
</span>757.129<span style="">    </span>26.4936<span style="">    </span>26.4578 -0.0149128<span style="">   </span>-4.77214</p>

<p class="MsoNormal">Coulomb-14<span style="">                
</span>-199.523<span style="">     </span>14.949<span style="">     </span>14.158 -0.0519427<span style="">   </span>-16.6218</p>

<p class="MsoNormal">LJ (SR)<span style="">                    
</span>-2670.5<span style="">    </span>111.201<span style="">    </span>109.688<span style="">   
</span>0.19784<span style="">    </span>63.3092</p>

<p class="MsoNormal">Coulomb (SR)<span style="">               
</span>739.794<span style="">    </span>16.1807<span style="">    </span>15.4473<span style=""> 
</span>0.0521352<span style="">    </span>16.6834</p>

====================================================<br />pbc              =  xyz                   <br /><br />        <br />;        Run control                    <br />integrator          =  md                    <br />

dt                  =  0.002                <br />nsteps              =  1000000 ;5000          <br />nstcomm             =  100                <br /><br />;        Output control<br />nstenergy           =  100                  <br />




nstxout             =  100                 <br />nstvout             =  0<br />nstfout             =  0<br />nstlog              =  1000                 <br />nstxtcout          =  1000                 <br /><br />;        Neighbor searching<br />




nstlist             =  10                <br />ns_type             =  grid                <br /><br />;        Electrostatics/VdW <br />coulombtype         =  PME                     <br />vdw-type            =  Shift              <br />




rcoulomb-switch     =  0                   <br />rvdw-switch         =  0.9 ;0                <br /><br />;        Cut-offs<br />rlist               =  1.25                 <br />rcoulomb            =  1.25 ;1.1             <br />rvdw                =  1.0                 <br />




<br />;        PME parameters<br />fourierspacing      =  0.3                 <br />fourier_nx          =  0<br />fourier_ny          =  0<br />fourier_nz          =  0<br />pme_order          =  4                 <br />ewald_rtol         =  1e-5<br />




optimize_fft      =  yes<br /><br />;        Temperature coupling    <br />Tcoupl              =  v-rescale                  <br />tc-grps             =  System  ;HEX               <br />tau_t               =  0.1     ;0.1                   <br />




ref_t               =  400     ;300              <br /><br />;        Pressure coupling<br />Pcoupl              =  Parrinello-Rahman             <br />Pcoupltype          =  isotropic                  <br />tau_p               =  1      1           ;0.5          <br />




compressibility     =  4.5e-5 4.5e-5           <br />ref_p               =  70    70                   <br /><br />;        Velocity generation               <br />gen_vel             =  yes                <br />gen_temp            =  300.0                <br />




gen_seed            =  173529                <br /><br />;        Bonds<br />constraints             = all-bonds              <br />constraint-algorithm = lincs<br />
</div></blockquote>