<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>I've started using version 4.5.4 of gromacs, having previously been using version 4.0 on an older server.</div><div><br></div><div>When I run a simulation on v4.0 everything seems to run fine. However, when I run the same simulation on v4.5.4, mdrun gives me the error message:</div><div><br></div><div>########################################################################</div><div><br></div><div><div>Making 3D domain decomposition 4 x 3 x 2</div><div>starting mdrun 'PROTEIN IN BILAYER'</div><div>5000000 steps, 150000.0 ps.</div><div>step 0</div><div>Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292 1.0122</div></div><div><br></div><div><div>Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292 1.0122</div></div><div><br></div><div><div>.</div><div>.</div><div>.</div><div>.</div><div>Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292 1.0122</div><div><br></div><div>Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061 1.02015</div><div><br></div><div>Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061 1.02015</div><div>.</div></div><div>.</div><div>.</div><div><div>Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061 1.02015</div><div><br></div><div>Step 25, time 0.75 (ps) LINCS WARNING</div><div>relative constraint deviation after LINCS:</div><div>rms 0.000004, max 0.000015 (between atoms 147 and 148)</div><div>bonds that rotated more than 30 degrees:</div><div> atom 1 atom 2 angle previous, current, constraint length</div><div> 178 179 34.7 0.2600 0.2600 0.2600</div><div><br></div><div>Step 28, time 0.84 (ps) LINCS WARNING</div><div>relative constraint deviation after LINCS:</div><div>rms 19.241184, max 126.849724 (between atoms 35 and 36)</div><div>bonds that rotated more than 30 degrees:</div><div> atom 1 atom 2 angle previous, current, constraint length</div><div><br></div><div>Step 28, time 0.84 (ps) LINCS WARNING</div><div>relative constraint deviation after LINCS:</div><div>rms 1.739422, max 8.610986 (between atoms 496 and 497)</div><div>bonds that rotated more than 30 degrees:</div><div> atom 1 atom 2 angle previous, current, constraint length</div><div> 45 46 90.0 0.2650 0.5083 0.2650</div><div> 35 36 90.0 0.3100 39.6334 0.3100</div><div> 42 43 90.0 0.2600 1.2129 0.2600</div><div> 45 46 90.0 0.2650 0.5083 0.2650</div><div> 482 483 90.0 0.2600 0.8649 0.2600</div><div> 496 497 90.0 0.2700 2.5950 0.2700</div><div> 496 498 90.0 0.2700 1.4511 0.2700</div><div> 497 498 90.0 0.2700 2.5822 0.2700</div><div>Wrote pdb files with previous and current coordinates</div><div>Wrote pdb files with previous and current coordinates</div><div>Segmentation fault</div></div><div><br></div><div><div>########################################################################</div></div><div><br></div><div><br></div><div>I've run g_gmxdump/gmxdump to get the input parameters for the simulations using the 2 different versions, which I can't attach because they're too big but which differ in the lines shown below (v4.0 on the left and v4.5.4 on the right):</div><div><br></div><div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstcomm = 1</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstcomm = 10</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstcalcenergy = 1</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstcalcenergy = 10</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nsttcouple = 1</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nsttcouple = 10</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstpcouple = 1</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstpcouple = 10</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> rgbradii = 2</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> rgbradii = 1</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> sa_surface_tension = 2.092</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> sa_surface_tension = 2.05016</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> sc_sigma_min = 0</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> sc_sigma_min = 0.3</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstdhdl = 1</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> |</span></font></font><span class="Apple-tab-span" style="white-space: pre; "><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> </span></font></font></span><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "> nstdhdl = 10</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'" size="2"><span class="Apple-style-span" style="font-size: 10px; "><br></span></font></div></div><div><br></div><div>and also for cmap atomtypes values:</div><div>in v4.0:</div><div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 0]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 1]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 2]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 3]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 4]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 5]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 6]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 7]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 8]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 9]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 10]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 11]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 12]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 13]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 14]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 15]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 16]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 17]={radius= 0.00000e+00, volume= 0.00000e+00, gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct= 0.00000e+00)}</span></font></font></div></div><div><br></div><div>and in v4.1</div><div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 0]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 1]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 2]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 3]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 4]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 5]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 6]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 7]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 8]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 9]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 10]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 11]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 12]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 13]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 14]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 15]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 16]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> atomtype[ 17]={radius=-1.00000e+00, volume=-1.00000e+00, gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=-1.00000e+00)}</span></font></font></div></div><div><br></div><div><br></div><div>I haven't set any of these values and I don't understand why the default values for parameters such as nsttcouple differ by a factor of 10. I know that in v4.5.4 parameters such as nsttcouple are by default set to be equal to nstlist (which =10 in my simulations) but I don't understand how the default is being set in v4.0. </div><div><br></div><div>The larger nstpcouple default values seem to me like the cause of my warning messages and eventual crash of the system when run in v4.5.4 but I am also worried that I don't know how the cmap atomtypes values are being set and how these differences will affect the simulations. Do you have any pointers?</div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px; "><br></span></font></font></div><div><font class="Apple-style-span" face="'Courier New'"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px; "><br></span></font></font></div><div>Many thanks,</div><div><br></div><div>Anna</div></body></html>