[gmx-users] pdb2gmx -vsite h hangs
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 10 12:18:05 CET 2009
Ilya Chorny wrote:
> Justin,
>
> Thanks for pointing me to section 6.5. I am running ~500K atoms because
> I want to test the scaling as well.
>
What I mean was, when reporting problems to the list, make the test case small
so you eliminate variables like available system memory. Furthermore, it is
unnecessary to process a pure water system with pdb2gmx; just create a topology
for one water molecule and fix the topol.top to correspond to however many
molecules there are.
> So I'm confused. How can I use pdb2gmx -vsite h this to run a protein
> and water simulation with a 4fs timestep as described in the Gromacs
> 4.0 paper if -vsite does not apply to OH/NH hydrogens. They don't
> describe using heavyh in the paper and there are earlier posts that
> teach away from using heavyh.
>
The timestep derives primarily from the use of constraints, I believe. The
LINCS algorithm is stable up to 5 fs, IIRC. Do some tests with 2, 4, and 5 fs
to determine if you are satisfied with energy conservation.
-Justin
> Thanks,
>
> Ilya
>
>
> On Mon, Mar 9, 2009 at 7:53 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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>
>
>
> --
> 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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