[gmx-users] pdb2gmx -vsite h hangs

[Ilya Chorny]

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.
I created a water box with ~500K atoms.

I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol

I get the following output at which point it hangs. I waited for about 2 hrs
before killing it.

Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/elements.dat
Entries in elements.dat: 218
Reading water_solv.gro...
Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984',
587676 atoms
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 0 chains and 1 blocks of water and 195892 residues with 587676
atoms

  chain  #res #atoms
  1 '-' 195892 587676  (only water)

No occupancies in water_solv.gro
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp
Residue 56
Sorting it all out...
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (587676 atoms, 195892 residues)
There are 195892 donors and 195892 acceptors
There are 280210 hydrogen bonds
Checking for duplicate atoms....
Opening library file
/data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat
7 out of 7 lines of specbond.dat converted succesfully

Thanks,

Ilya


-- 
Ilya Chorny Ph.D.




-- 
Ilya Chorny Ph.D.
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