[gmx-users] pdb2gmx -vsite h hangs

[Justin A. Lemkul]

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.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================