Ilya Chorny wrote:
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.
From the manual, section 6.5: "For the hydrogens in water and in hydroxyl,
sulfhydryl or amine groups, no degrees of freedom can be removed, because
rotational freedom should be preserved. The only other option available to slow
down these motions, is to increase the mass of the hydrogen atoms at the expense
of the mass of the connected heavy atom."
Try pdb2gmx -heavyh.
When diagnosing a problem, make it simple. Processing 500,000 atoms may indeed
take a long time. If you create a test case with a single water molecule and
write the topology, pdb2gmx actually completes successfully, however, per the
quote above, no virtual sites are generated.
-Justin
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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