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 <[email protected]> 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. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Ilya Chorny Ph.D.
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