[gmx-users] pdb2gmx -vsite h hangs

[Ilya Chorny]

Justin,

Thanks for pointing me to section 6.5. I am running ~500K atoms because I
want to test the scaling as well.
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.

Thanks,

Ilya


On Mon, Mar 9, 2009 at 7:53 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Ilya Chorny Ph.D.
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