<div class="gmail_quote"><br><p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;"> </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">I am trying to do the NPT
equilibration of a cyclic peptide in DMSO solvent BOX using all atom charm force
field (ffcharmm27) on GROMACS. <span> </span>The NVT
equilibration is working but the NPT equilibration shows the following ERROR. </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Back Off! I just backed up
results/eq50K.log to results/#eq50K.log.1#</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Reading</span><span style="font-size: 10pt; font-family: "Courier New";"> file in1bar50K.tpr, VERSION
4.0.5 (double precision)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Back Off! I just backed up
results/eq50K.trr to results/#eq50K.trr.1#</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Back Off! I just backed up
results/eq50K.xtc to results/#eq50K.xtc.1#</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Back Off! I just backed up
results/eq50K.edr to results/#eq50K.edr.1#</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">starting mdrun '16CHA in
DMSO'</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">25000 steps,<span> </span>50.0 ps.</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">[2]<span> </span>Done<span> </span>nedit eq.csh</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #45 atoms 44 and
46</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #45 atoms 44 and
46</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #48 atoms 46 and
52</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #34 atoms 34 and
35</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Warning: 1-4 interaction
between 26 and 36 at distance 153.333 which is larger than the 1-4 table size
2.400 nm</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">These are ignored for the
rest of the simulation</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">This usually means your
system is exploding,</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">if not, you should increase
table-extension in your mdp file</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">or with user tables increase
the table size</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Step 632<span> </span>Warning: pressure scaling more than 1%, mu:
190.046 190.046 190.046</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #39 atoms 38 and
39</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Step 633<span> </span>Warning: pressure scaling more than 1%, mu:
252.207 252.207 252.207</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #8 atoms 6 and 12</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Step 634<span> </span>Warning: pressure scaling more than 1%, mu:
1.23498 1.23498 1.23498</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Inner product between old
and new vector <= 0.0!</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">constraint #5 atoms 2 and 5</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Wrote pdb files with
previous and current coordinates</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">There were 2 inconsistent
shifts. Check your topology</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">-------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Program mdrun, VERSION 4.0.5</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Source code file: nsgrid.c,
line: 348</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Fatal error:</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">Number of grid cells is
zero. Probably the system and box collapsed.</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">-------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">Corresponding .mdp file is as
follows. </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------START_[7.3]-----------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------GENERAL_[7.3.1]-------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*<span> </span>User </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*<span> </span>COMMENTS:</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------PREPROCESSING_[7.3.2]-------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>title<span> </span>= Free MD</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>cpp<span> </span>= /lib/cpp<span> </span>; Vorprozessor</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;include<span> </span>;
Einfuegen von Topology-File-Verzeichnissen </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;define<span> </span><span> </span>= <span> </span>;
genaue Definition des Top-Files, z.B. Restraints</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------RUN_CONTROL_[7.3.3]---------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span></span><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">integrator<span> </span>= md<span> </span>; Algorithmus: steep empfolen</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;tinit </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>dt<span> </span>= 0.002<span> </span>; [ZEIT: 0.001] Integrationsschritte
in ps !</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nsteps<span> </span>= 250000<span> </span>; [SCHRITTE: 0] Summe aller
Integrationsschritte (aktuell: 10ps)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;init_step </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>comm_mode<span> </span><span> </span>= linear</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstcomm<span> </span>= 500<span> </span>; [SCHRITTE: 1] Frequenz der Massenzentrumsbewegung</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>comm_grps<span> </span>= system</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*-------------LANGEVIN_DYNAMICS_[7.3.4]---------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;bd_temp</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;bd_fric</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>ld_seed<span> </span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------ENERGY_MINIMIZATION_[7.3.5]-------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;emtol<span> </span><span> </span>= 100</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;emstep<span> </span><span> </span>= 0.01</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;nstcgsteep<span> </span>= 50</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;nbfgscorr<span> </span><span> </span>= 10</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------SHELL_MOLECULAR_DYNAMICS_[7.3.6]--------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;emtol</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;niter<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*-------------OUTPUT_CONTROL_[7.3.7]------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstxout<span> </span>= 50000 <span> </span>; [SCHRITTE: 100] Frequenz des
Schreibens der Koordinaten</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstvout<span> </span>= 50000<span> </span>; [SCHRITTE: 100] Frequenz des Schreibens der
Geschwindigkeiten</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstfout<span> </span>= 50000<span> </span>; [SCHRITTE:<span> </span>0]
Frequenz des Schreibens der Kraefte</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstlog<span> </span>= 50000<span> </span>; [SCHRITTE: 100] Frequenz des
Schreibens der Energien (in log-File)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span>nstenergy<span> </span>= 500<span> </span>; [SCHRITTE: 100] Frequenz des Schreibens der
Energien (in Energy-File)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span></span><span style="font-size: 10pt; font-family: "Courier New";">nstxtcout<span> </span>= 500</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>xtc_precision<span> </span>= 1000</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>xtc_grps<span> </span>= 16CHA</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>energygrps<span> </span>= 16CHA DMSO</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------NEIGHBOUR_SEARCHING_[7.3.8]-------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span></span><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">nstlist<span> </span>= 5<span> </span>; [SCHRITTE: 10] Frequenz des Updates der
Neighbour-List</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE"><span> </span></span><span style="font-size: 10pt; font-family: "Courier New";">ns_type<span> </span>= grid<span> </span>; Neighbour-Listen-Typ</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>pbc<span> </span><span> </span>= xyz</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>rlist<span> </span><span> </span>= 0.8</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;domain-decomposition<span> </span>= no</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*-------------ELECTROSTATIC_&_VDW_[7.3.9]-------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>coulombtype<span> </span><span> </span>= reaction-field</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;rcoulomb_switch<span> </span>= 0.0</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>rcoulomb<span> </span>= 1.4</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;epsilon_r<span> </span>= 1</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>epsilon_rf<span>
</span><span> </span>= 38</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>vdwtype<span> </span>= cut-off</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;rvdw_switch<span> </span>= 0.0</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>rvdw<span> </span>= 1.4</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;dispcorr<span> </span><span>
</span>=</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;table-extension</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;fourierspacing<span> </span>= 0.12</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;(fourier_nx ;fourier_ny;
fourier_nz)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;pme_order<span> </span>= 4</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;ewald_rtol<span> </span>= 1e-06</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;epsilon_surface<span> </span>= 0</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;ewald_geometry</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>optimize_fft<span> </span>= yes</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*--------------TEMPERATURE_COUPLING_[7.3.10]-----------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>tcoupl<span> </span>= v-rescale</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>tc_grps<span>
</span><span> </span><span> </span>= system</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>tau_t<span> </span>= 0.1</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>ref_t<span> </span>= 50</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*--------------PRESSURE_COUPLING_[7.3.11]--------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>pcoupl<span> </span>= berendsen</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>pcoupltype<span> </span>= isotropic</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>tau_p<span> </span>= 2.0</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>compressibility<span> </span>= 5.22e-05<span> </span>; DMSO isothermal compressibility (for Water: 4.50e-05 bar-1)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>ref_p<span> </span>= 1.0</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------SIMULATED_ANNEALING_[7.3.12]-----------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;annealing</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;annealing_npoints</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;annealing_time</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;annealing_temp</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------VELOCITY_
GENERATION_[7.3.13]----------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>gen_vel<span>
</span><span> </span>= no</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>gen_temp<span> </span>= 50</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>gen_seed<span> </span>= 173529</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------BONDS_[7.3.14]-------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>constraints<span> </span>= all-bonds</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>constraint_algorithm<span> </span>= shake</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>continuation<span> </span>= yes</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"><span> </span>shake_tol<span> </span><span> </span>= 0.0001</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;lincs_order<span> </span>= 4</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;lincs_iter<span> </span>= 1</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;lincs_warnangle<span> </span>= 30</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;morse</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------ENERGY_GROUP_EXCLUSIONS_[7.3.15]-------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;energygrp_excl<span> </span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------NMR_REFINEMENT_[7.3.16]----------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;disre</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;disre_weighting</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;disre_mixed</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;disre_fc</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;disre_tau</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;nstdisreout</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;orire</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;orire_fc</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;orire_tau</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;orire_fitgrp</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;nstorireout</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;dihre<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;dihre_fc<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;dihre_tau<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;nstdihreout<span> </span></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------FREE_ENERGY_PERTURBATION_[7.3.17]------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;free_energy<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;init_lambda<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;delta_lambda<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;sc_alpha<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;sc_power<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;sc_sigma<span> </span><span>
</span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------NON-EQUILIBRIUM_MD_[7.3.18]------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;acc_grps</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;accelerate</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;freezegrps<span> </span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;freezedim<span> </span>= </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;cos_acceleration</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------ELECTRIC_FIELDS_[7.3.19]---------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;(E_x; E_y; E_z)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;(E_xt; E_yt; E_zt)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";" lang="DE">;*---------------USER_DEFINED_THINGIES_[7.3.20]---------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;(user1_grps; user2_grps)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;(userint1; userint2;
userint3; userint4)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;(userreal1; userreal2;
userreal3; userreal4)</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";">;*---------------END_[7.3]------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p><br><p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">I had a look on the archives list
already and implemented the earlier suggested remarks but still the problem persists.</span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;"> </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">Could you please suggest what could
be the problem?</span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;"> </span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">Regards,</span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span style="font-size: 14pt; line-height: 150%;">Uday.</span></p>
</div><br>