<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Hi,</span></p>
<p class="MsoNormal" style="text-indent:24.0pt"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif"">I am using Gromacs
4.5.4. After successful minimization by SD, I continued with equilibration step
but I got the below errors. I tried many times with different parameters but the
problem still persists. I have given errors and md parameters of equilibration
step below. I have also provided my minimization output at the end. Could you
provide some suggestions what went wrong?. </span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Many thanks</span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Sincerely</span></p>
<p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Hendry </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:16.0pt;font-family:"Times New Roman","serif"">Errors:</span></b></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Warning:
1-4 interaction between 2969 and 2974 at distance 5.543 which is larger than
the 1-4 table size 2.400 nm</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">These
are ignored for the rest of the simulation</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">This
usually means your system is exploding,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">if
not, you should increase table-extension in your mdp file</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">or
with user tables increase the table size</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Step
1, time 0.002 (ps) LINCS WARNING</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">relative
constraint deviation after LINCS:</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">rms
92.242942, max 9194.071289 (between atoms 3025 and 3024)</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">bonds
that rotated more than 30 degrees:</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> atom 1 atom 2
angle previous, current,
constraint length</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2987
2973 106.3 1.3892
7.3433 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2974
2973 174.8 1.1940
7.7482 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2975
2974 79.9 0.1865
1.4460 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2978
2975 98.5 0.1423
0.6164 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2982
2978 86.1 0.1421
0.6512 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2979
2978 89.8 0.1114
5.2456 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2989
2987 132.2 0.1781
2.6697 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2988
2987 142.2 0.2284
2.7180 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2971
2969 62.9 7.0921
3.5084 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2970
2969 88.1 6.8598
4.7791 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2973
2971 120.6 2.8109
8.8274 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2972
2971 165.6 2.0293
6.9953 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3016
3013 103.1 0.5628
65.6450 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3014
3013 39.0 0.3331
5.0018 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3017
3014 81.6 0.1827
57.9252 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3015
3014 77.9 0.0752
6.3613 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3020
3016 81.3 2.2255
79.7378 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3019
3016 100.9 0.4862
54.4883 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3019
3017 79.3 0.1679
57.8415 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3018
3017 94.5 0.1686
66.3440 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3022
3019 87.7 0.5657
7.7539 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3026
3022 104.5 0.8085
54.9923 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3023
3022 87.4 0.6108
5.0641 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2968
2964 174.1 1.5617
5.1413 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2965
2964 59.5 5.2178
4.0658 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2969
2965 35.5 7.6693
2.9000 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2966
2965 137.3 5.3225
4.6157 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2967
2966 150.3 1.6016
1.7332 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2968
2967 72.4 0.1685
1.8310 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3026
3024 94.8 0.8572
96.6156 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3025
3024 89.9 0.6811 1002.2628 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3027
3026 108.0 1.1638
47.5384 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2991
2989 138.2 0.2045
0.6556 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2990
2989 157.0 0.1236
0.7213 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2998
2991 89.9 0.1961
0.9471 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2992
2991 79.5 0.1931
0.5434 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2993
2992 49.8 0.1577
0.1862 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3000
2998 84.9 0.1463
0.5492 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2999
2998 83.3 0.1346
0.5372 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3002
3000 44.2 0.1535
0.2150 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3003
3002 31.6 0.1548
0.1834 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3009
3007 62.4
0.1507 0.3181 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3008
3007 44.1 0.1280
0.1578 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3011
3009 80.3 0.2401
1.9894 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3010
3009 82.9 0.1141
0.3157 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3028
3011 85.2 0.2391
1.9233 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3012
3011 97.9 0.3034
4.9831 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3013
3012 82.4 0.3759
7.3991 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3024
3020 85.6 2.4674
98.3412 0.1390</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3021
3020 81.0 1.2452
66.1375 0.1090</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3030
3028 88.9 0.1492
0.2673 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 3029
3028 61.2 0.1379
0.2407 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 49372
49371 89.5 0.1000 221.0566 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 49373
49371 92.4 0.1000 170.7231 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2956
2954 153.4 0.1550
3.5621 0.1470</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2955
2954 135.5 0.1246
0.8967 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2962
2956 76.6 0.7151
5.0532 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2957
2956 178.7 0.1220
3.9773 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2958
2957 155.0 0.2036
1.2639 0.1530</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2961
2959 34.5 0.1265
0.1186 0.1250</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2960
2959 30.4 0.1264
0.1346 0.1250</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2964
2962 114.9 1.7422
7.9205 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2963
2962 156.9 0.4832
6.1127 0.1230</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 53158
53157 90.0 0.1000
0.1575 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 53159
53157 90.0 0.1000
0.1747 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 53386
53385 90.0 0.1000
0.1537 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 53387
53385 56.5 0.1000
0.0962 0.1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> 2954
2952 68.7 0.1615
0.7870 0.1330</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Back
Off! I just backed up step1b_n2.pdb to ./#step1b_n2.pdb.1#</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Back
Off! I just backed up step1c_n2.pdb to ./#step1c_n2.pdb.1#</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Wrote
pdb files with previous and current coordinates</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">-------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Program
mdrun, VERSION 4.5.4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Source
code file: pme.c, line: 538</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Fatal
error:</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">10
particles communicated to PME node 2 are more than 2/3 times the cut-off out of
the domain decomposition cell of their charge group in dimension x.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">This
usually means that your system is not well equilibrated.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">For
more information and tips for troubleshooting, please check the GROMACS</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">website
at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">-------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">"They
Were So Quiet About It" (Pixies)</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Error
on node 2, will try to stop all the nodes</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Halting
parallel program mdrun on CPU 2 out of 4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">gcq#37:
"They Were So Quiet About It" (Pixies)</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">--------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">MPI_ABORT
was invoked on rank 2 in communicator MPI_COMM_WORLD</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">with
errorcode -1.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">NOTE:
invoking MPI_ABORT causes Open MPI to kill all MPI processes.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">You
may or may not see output from other processes, depending on</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">exactly
when Open MPI kills them.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">--------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">--------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">mpirun
has exited due to process rank 2 with PID 30681 on</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">node
ymu039-107 exiting without calling "finalize". This may</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">have
caused other processes in the application to be</span></p>
<div style="border:none;border-bottom:solid windowtext 1.0pt;padding:0cm 0cm 1.0pt 0cm">
<p class="MsoNormal" style="border:none;padding:0cm"><span lang="EN-US" style="font-family:"Times New Roman","serif"">terminated by signals sent by
mpirun (as reported here).</span></p>
</div>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:16.0pt;font-family:"Times New Roman","serif"">Equilibration parameters</span></b></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">title =
TM1 in a POPC bilayer at 100K</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">cpp = /lib/cpp</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">integrator = md</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">define =
-DPO1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; Output</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">dt = 0.002
; ps !</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nsteps = 100000 ; total 200 ps.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstcomm = 1</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstxout = 5000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstvout = 5000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstfout = 0</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstlog = 500</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstenergy = 500</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstxtcout = 500</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">xtc_precision = 1000</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; Electrostatics and VdW</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">nstlist
= 5</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">pbc = xyz</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">rlist
= 1.2</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">coulombtype
= PME</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">rcoulomb = 1.2</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">fourierspacing
= 0.16</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">pme_order
= 4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">rvdw
= 1.4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">constraints
= all-bonds</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">optimize_fft
= yes</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">constraint-algorithm =
lincs</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">lincs-order
= 4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">lincs_iter
= 1</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; berendsen temperature coupling</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Tcoupl
= berendsen</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">tc-grps
= Protein POPC SOL CL</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">tau_t
= 0.1 0.1
0.1 0.1</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">ref_t
= 100 100
100 100</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; Energy monitoring</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">energygrps
= Protein POPC SOL CL</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; Isotropic pressure coupling</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">pcoupl =
parrinello-rahman</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">pcoupltype
= semiisotropic</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">tau_p
= 1.0</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">compressibility
= 4.5e-5 4.5e-5
</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">ref_p
= 1.0 1.0</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">; Generate velocity is on 100K</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">gen_vel
= yes</span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">gen_temp = 100.0</span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">gen_seed = 173529</span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><b><span style="font-size:16.0pt;font-family:"Times New Roman","serif"">SD minimization ouput:</span></b></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Steepest Descents converged to Fmax < 1000 in 23239
steps</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Potential Energy =
-1.0507182e+06</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman","serif"">Maximum force = 9.8500549e+02 on atom 5087</span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Norm of force =
2.4736889e+01</span></p>