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<p class="MsoNormal">Hello,</p><p class="MsoNormal"><br></p><p class="MsoNormal">I pull molecule into membrane by MD simulations but it error about<br></p><p class="MsoNormal"><br></p><p class="MsoNormal">processing topology...</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ffgmxbon.itp</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ff_dum.itp</p>
<p class="MsoNormal">Generated 1284 of the 1485 non-bonded parameter combinations</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/spc.itp</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ions.itp</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_A'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_B'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_C'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_D'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_E'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_F'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_G'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_H'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_I'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_J'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_K'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_L'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_M'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_N'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_O'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_P'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_Q'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_R'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_S'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_T'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_U'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_V'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_W'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_X'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_Y'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein_Z'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'Protein'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 2 bonded neighbours molecule type 'SOL'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">Excluding 3 bonded neighbours molecule type 'VIV'</p>
<p class="MsoNormal">turning all bonds into constraints...</p>
<p class="MsoNormal">processing coordinates...</p>
<p class="MsoNormal">double-checking input for internal consistency...</p>
<p class="MsoNormal">Velocities were taken from a Maxwell distribution at 325 K</p>
<p class="MsoNormal">renumbering atomtypes...</p>
<p class="MsoNormal">converting bonded parameters...</p>
<p class="MsoNormal">initialising group options...</p>
<p class="MsoNormal">processing index file...</p>
<p class="MsoNormal">Analysing residue names:</p>
<p class="MsoNormal">Opening library file
/home/Ell/gromacMPI/share/gromacs/top/aminoacids.dat</p>
<p class="MsoNormal">There are:<span style=""> </span>3784<span style=""> </span>OTHER residues</p>
<p class="MsoNormal">There are:<span style=""> </span>0<span style=""> </span>PROTEIN residues</p>
<p class="MsoNormal">There are:<span style=""> </span>0<span style=""> </span>DNA residues</p>
<p class="MsoNormal">Analysing Other...</p>
<p class="MsoNormal">Pull group 0 'DPP' has 6400 atoms</p>
<p class="MsoNormal">Pull group 1 'VIV' has 32 atoms</p>
<p class="MsoNormal">Making dummy/rest group for Acceleration containing 17397
elements</p>
<p class="MsoNormal">Making dummy/rest group for Freeze containing 17397 elements</p>
<p class="MsoNormal">Making dummy/rest group for Energy Mon. containing 17397
elements</p>
<p class="MsoNormal">Making dummy/rest group for VCM containing 17397 elements</p>
<p class="MsoNormal">Number of degrees of freedom in T-Coupling group DPP is
12926.89</p>
<p class="MsoNormal">Number of degrees of freedom in T-Coupling group VIV is
62.99</p>
<p class="MsoNormal">Number of degrees of freedom in T-Coupling group SOL is
21928.12</p>
<p class="MsoNormal">Making dummy/rest group for User1 containing 17397 elements</p>
<p class="MsoNormal">Making dummy/rest group for User2 containing 17397 elements</p>
<p class="MsoNormal">Making dummy/rest group for XTC containing 17397 elements</p>
<p class="MsoNormal">Making dummy/rest group for Or. Res. Fit containing 17397
elements</p>
<p class="MsoNormal">Making dummy/rest group for QMMM containing 17397 elements</p>
<p class="MsoNormal">T-Coupling<span style=""> </span>has 3
element(s): DPP VIV SOL</p>
<p class="MsoNormal">Energy Mon.<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">Acceleration<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">Freeze<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">User1<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">User2<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">VCM<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">XTC<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">Or. Res. Fit<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">QMMM<span style=""> </span>has 1
element(s): rest</p>
<p class="MsoNormal">Checking consistency between energy and charge groups...</p>
<p class="MsoNormal">Calculating fourier grid dimensions for X Y Z</p>
<p class="MsoNormal">Using a fourier grid of 13x13x14, spacing 0.490 0.492 0.477</p>
<p class="MsoNormal">Pull group<span style="">
</span>natoms<span style=""> </span>pbc atom<span style=""> </span>distance at start<span style=""> </span>reference at t=0</p>
<p class="MsoNormal"><span style=""> </span>0<span style=""> </span>6400<span style="">
</span><span style=""> </span>3200</p>
<p class="MsoNormal"><span style=""> </span>1<span style=""> </span>32<span style="">
</span>17381<span style=""> </span>2.401<span style=""> </span>-99999.422</p>
<p class="MsoNormal">Estimate for the relative computational load of the PME mesh
part: 0.49</p>
<p class="MsoNormal">This run will generate roughly 3 Mb of data</p>
<p class="MsoNormal">writing run input file...</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">There was 1 warning</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-------------------------------------------------------</p>
<p class="MsoNormal">Program grompp_mpi, VERSION 4.0.2</p>
<p class="MsoNormal">Source code file: gmx_fatal.c, line: 481</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Fatal error:</p>
<p class="MsoNormal">Too many warnings (1), grompp_mpi terminated.</p>
<p class="MsoNormal">If you are sure all warnings are harmless, use the -maxwarn
option.</p>
<p class="MsoNormal">-------------------------------------------------------</p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Have a nice day</p>Wara
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