<div>Justin,</div><div><br></div>Thanks for pointing me to section 6.5. I am running ~500K atoms because I want to test the scaling as well. <div><br></div><div>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. </div>
<div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br><br><div class="gmail_quote">On Mon, Mar 9, 2009 at 7:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Ilya Chorny wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
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. <br>
</blockquote>
<br></div>
>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."<br>
<br>
Try pdb2gmx -heavyh.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
I created a water box with ~500K atoms. <br>
I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol<br>
<br>
I get the following output at which point it hangs. I waited for about 2 hrs before killing it.<br>
<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/elements.dat<br>
Entries in elements.dat: 218<br>
Reading water_solv.gro...<br>
Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 587676 atoms<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat<br>
26 out of 26 lines of xlateat.dat converted succesfully<br>
Analyzing pdb file<br>
There are 0 chains and 1 blocks of water and 195892 residues with 587676 atoms<br>
<br>
chain #res #atoms<br>
1 '-' 195892 587676 (only water)<br>
<br>
No occupancies in water_solv.gro<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp<br>
Atomtype 1<br>
Reading residue database... (ffoplsaa)<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp<br>
Residue 56<br>
Sorting it all out...<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb<br>
<br>
Back Off! I just backed up topol.top to ./#topol.top.2#<br>
Processing chain 1 (587676 atoms, 195892 residues)<br>
There are 195892 donors and 195892 acceptors<br>
There are 280210 hydrogen bonds<br>
Checking for duplicate atoms....<br>
Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat<br>
7 out of 7 lines of specbond.dat converted succesfully<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
<br>
-- <br>
Ilya Chorny Ph.D.<br>
<br>
<br>
<br>
<br>
-- <br>
Ilya Chorny Ph.D.<br>
<br>
<br></div></div>
------------------------------------------------------------------------<div class="im"><br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>
</div>