Hi, all!<div><br></div><div>I am trying to simulate a system of peptide, water, NaCl and DMSO.</div><div>I used pdb2gmx to generate .top file for DMSO and then created this .itp:</div><div>(initial DMSO structure had been minimized before it was used for box generation)</div>
<div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">[ moleculetype ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; Name nrexcl</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">DMSO 3</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"><br></font></div><div>
<font class="Apple-style-span" face="'courier new', monospace" size="1">[ atoms ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; nr type resnr residue atom cgnr charge mass typeB chargeB massB</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">; residue 1 DMSO rtp DMSO q 0.0</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 1 SDmso 1 DMSO SDmso 1 0.12753 32.06 ; qtot 0.1275</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 2 ODmso 1 DMSO ODmso 1 -0.44753 15.9994 ; qtot -0.32</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 3 CDmso 1 DMSO CDms1 1 0.16 15.035 ; qtot -0.16</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 4 CDmso 1 DMSO CDms2 1 0.16 15.035 ; qtot 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">[ bonds ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; ai aj funct c0 c1 c2 c3</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 1 2 2 gb_41</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 1 3 2 gb_42</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 1 4 2 gb_42</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 2 3 2 gb_49</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 2 4 2 gb_49</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 3 4 2 gb_50</font></div>
</div><div><br></div><div>Corresponding record in /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp is:</div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">[ DMSO ]</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> [ atoms ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">SDmso SDmso 0.12753 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">ODmso ODmso -0.44753 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">CDms1 CDmso 0.16000 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">CDms2 CDmso 0.16000 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> [ bonds ]</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">SDmso ODmso gb_41 </font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">SDmso CDms1 gb_42 </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">SDmso CDms2 gb_42 </font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">ODmso CDms1 gb_49 </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">ODmso CDms2 gb_49 </font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">CDms1 CDms2 gb_50 </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> [ angles ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; ai aj ak gromos type</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> [ impropers ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; ai aj ak al gromos type</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> [ dihedrals ]</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; ai aj ak al gromos type</font></div>
</div><div><br></div><div>Then I created box with genbox using -ci and -cs options. I did add following strings in system .top file:</div><div>before [ system ]</div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; Include DMSO topology</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">#include "dmso.itp"</font></div></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"><br>
</font></div><div>after [ molecules ]</div><div><br></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">DMSO 69</font></div><div><br></div><div>Parameters what I used for energy minimization was:</div>
<div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; Parameters describing how to find the neighbors of each atom and how to calculate the interactions</font></div><div>
<font class="Apple-style-span" face="'courier new', monospace" size="1">nstlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 1<span class="Apple-tab-span" style="white-space:pre"> </span>; Frequency to update the neighbor list and long range forces</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">ns_type<span class="Apple-tab-span" style="white-space:pre"> </span>= grid<span class="Apple-tab-span" style="white-space:pre"> </span>; Method to determine neighbor list (simple, grid)</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">rlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; Cut-off for making neighbor list (short range forces)</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">coulombtype<span class="Apple-tab-span" style="white-space:pre"> </span>= PME<span class="Apple-tab-span" style="white-space:pre"> </span>; Treatment of long range electrostatic interactions</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">pme_order<span class="Apple-tab-span" style="white-space:pre"> </span>= 4<span class="Apple-tab-span" style="white-space:pre"> </span>; cubic interpolation</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">fourierspacing<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.12<span class="Apple-tab-span" style="white-space:pre"> </span>; grid spacing for FFT</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">rcoulomb<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; Short-range electrostatic cut-off</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">rvdw<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; Short-range Van der Waals cut-off</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">pbc<span class="Apple-tab-span" style="white-space:pre"> </span>= xyz <span class="Apple-tab-span" style="white-space:pre"> </span>; Periodic Boundary Conditions (yes/no)</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">; Dispersion correction</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">DispCorr<span class="Apple-tab-span" style="white-space:pre"> </span>= EnerPres<span class="Apple-tab-span" style="white-space:pre"> </span>; account for cut-off vdW scheme</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">constraint_algorithm = lincs<span class="Apple-tab-span" style="white-space:pre"> </span>; holonomic constraints </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">constraints<span class="Apple-tab-span" style="white-space:pre"> </span>= all-bonds<span class="Apple-tab-span" style="white-space:pre"> </span>; all bonds (even heavy atom-H bonds) constrained</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">lincs_iter<span class="Apple-tab-span" style="white-space:pre"> </span>= 1<span class="Apple-tab-span" style="white-space:pre"> </span>; accuracy of LINCS</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">lincs_order<span class="Apple-tab-span" style="white-space:pre"> </span>= 4<span class="Apple-tab-span" style="white-space:pre"> </span>; also related to accuracy</font></div>
</div><div><br></div><div>Then I get minimization crushed after such warnings:</div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">Step 0, time 0 (ps) LINCS WARNING</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">relative constraint deviation after LINCS:</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1">rms 0.646692, max 1.998582 (between atoms 237 and 236)</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1">bonds that rotated more than 30 degrees:</font></div><div><font class="Apple-style-span" face="'courier new', monospace" size="1"> atom 1 atom 2 angle previous, current, constraint length</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace" size="1"> 223 222 148.1 0.1535 0.0548 0.1530</font></div></div><div><br></div><div>When I set <font class="Apple-style-span" face="'courier new', monospace" size="1">constraints<span class="Apple-tab-span" style="white-space: pre; "> </span>= h-bonds </font>minimization was successful.</div>
<div><br></div><div>It seems LINCS algorithm has limitations on the molecule topology. I didn't know details of this method and need help.</div><div>What should I do for simulation works? Is there need to change DMSO topology or maybe it is better to use <span class="Apple-style-span" style="font-family: 'courier new', monospace; font-size: x-small; ">constraints</span><span class="Apple-tab-span" style="font-family: 'courier new', monospace; font-size: x-small; white-space: pre; "> </span><span class="Apple-style-span" style="font-family: 'courier new', monospace; font-size: x-small; ">= h-bonds</span> option?</div>
<div><br></div><div>Regards,</div><div>Yuri.</div><div><br></div>