<div class="gmail_quote"><br>Hi I am running 4.0.3. I wanted to test the 4fs timestep with virtual sites. I will be running a simulation with ~500K atoms. <div><br></div><div>I created a water box with ~500K atoms. </div><div>
<br></div><div>I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol</div>
<div><br></div><div>I get the following output at which point it hangs. I waited for about 2 hrs before killing it.</div><div><br></div><div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp</div>
<div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat</div><div>WARNING: masses will be determined based on residue and atom names,</div>
<div> this can deviate from the real mass of the atom type</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat</div><div>Entries in atommass.dat: 178</div><div>WARNING: vdwradii will be determined based on residue and atom names,</div>
<div> this can deviate from the real mass of the atom type</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat</div><div>Entries in vdwradii.dat: 28</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat</div>
<div>Entries in dgsolv.dat: 7</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat</div><div>Entries in electroneg.dat: 71</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/elements.dat</div>
<div>Entries in elements.dat: 218</div><div>Reading water_solv.gro...</div><div>Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 587676 atoms</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat</div>
<div>26 out of 26 lines of xlateat.dat converted succesfully</div><div>Analyzing pdb file</div><div>There are 0 chains and 1 blocks of water and 195892 residues with 587676 atoms</div><div><br></div><div> chain #res #atoms</div>
<div> 1 '-' 195892 587676 (only water)</div><div><br></div><div>No occupancies in water_solv.gro</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp</div><div>Atomtype 1</div>
<div>Reading residue database... (ffoplsaa)</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp</div><div>Residue 56</div><div>Sorting it all out...</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb</div>
<div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb</div><div><br></div><div>Back Off! I just backed up topol.top to ./#topol.top.2#</div>
<div>Processing chain 1 (587676 atoms, 195892 residues)</div><div>There are 195892 donors and 195892 acceptors</div><div>There are 280210 hydrogen bonds</div><div>Checking for duplicate atoms....</div><div>Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat</div>
<div>7 out of 7 lines of specbond.dat converted succesfully</div><div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br></div><br>-- <br>Ilya Chorny Ph.D.<br><br>
</div>
</div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>