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On 13/04/2011 2:10 AM, Anna Duncan wrote:
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<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>
</blockquote>
<br>
This looks like a standard case of <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>,
which can be quite situation dependent. In the absence of further
information, I'd guess that 4.0 got lucky with the numerical
integration, and 4.5.4 didn't.<br>
<br>
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<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, </div>
</blockquote>
<br>
gmxcheck is a good tool for comparing various file types.<br>
<br>
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<div>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>
</blockquote>
<br>
The heuristics by which these are set by default have changed. These
values are not of themselves indicative of a problem.<br>
<br>
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<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>
</blockquote>
<br>
These only matter if you're using the relevant algorithms, for which
the defaults have apparently changed.<br>
<br>
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<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>
</blockquote>
<br>
Since I don't think any native 4.0 forcefield used CMAP at all, I
infer you aren't, so this doesn't matter either.<br>
<br>
<blockquote
cite="mid:4ABEAAE5-3AD3-4AA5-888A-8EF4A7FDC005@mrc-mbu.cam.ac.uk"
type="cite">
<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>
</blockquote>
<br>
We don't know whether you're even using T-coupling, P-coupling or
CMAP. How about a quick description of your objective, simulation
system, equilibration protocol and maybe an .mdp file?<br>
<br>
In any case, until you've exhausted the diagnosis steps on the above
link, the smart money is betting that you have a somewhat unhappy
starting configuration.<br>
<br>
Mark<br>
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