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<div>Hi</div>
<div>After reading the log file and watching the trajectory movies(nstxout = 1), </div>
<div>some molecule clashes with another in my simulation system.</div>
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<div>How can i avoid the situation happening again?</div>
<div>How to modify the broken simulation?</div>
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<div>Thank you</div>
<div>Lin</div>
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<div>Message: 4<br>Date: Wed, 30 Dec 2009 19:00:51 -0500<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] some molecule clashing with another ?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4B3BE9B3.8020100@vt.edu">4B3BE9B3.8020100@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed</div>
<div> </div>
<div>Chih-Ying Lin wrote:<br>><br>><br>> Hi<br>> My simulation broke down and the simulation procedues are as follows.<br>><br>> 1. center a protein molecule in the simulation box<br>> 2. put 20 ligands around the protein with " genbox " command<br>
> 3. make sure that any atom of the ligands does not overlap on any atom<br>> of the protein with Visulization-software.<br>> 4. solvent addition , with the command " genbox *-vdwd* 0.2 "<br>> 5. Addition of ions, with the command " genion "<br>
> 6. Energy minimization of the solvated system<br>> 7. Position restrained MD<br>><br>> => simulation broke down.<br>> => It is very probable that some molecule clashing with another.</div>
<div>You can change "probable" to an actual answer if you analyze whatever LINCS<br>warnings are occurring (the atoms are listed) and by watching the resulting<br>trajectory.</div>
<div>> => since i have made sured that any atom of the ligands does not overlap<br>> on any atom of the protein with Visulization-software,<br>> the clashed pair of the molecules are possible " solvent vs<br>
> solvent " or "solvent vs protein" or "solvent vs<br>> ligand "</div>
<div>Then you should follow up #4 above with another visual inspection, as you did<br>with protein-ligand interactions, in addition to any information printed to the<br>log file (as above).</div>
<div>> => however, from the Gromacs manual , command "genbox"<br>> " Solvent molecules are removed from the box where the distance<br>> between any atom of the solute molecule(s) and any atom of the solvent<br>
> molecule is less<br>> than the sum of the VanderWaals radii of both atoms. A database<br>> (vdwradii.dat <<a href="http://manual.gromacs.org/current/online/dat.html">http://manual.gromacs.org/current/online/dat.html</a>>) of<br>
> VanderWaals radii is read by the program, atoms not in the<br>> database are assigned a default distance -vdw."<br>></div>
<div>So solvent-solvent overlap shouldn't be a problem.</div>
<div>> => here is vdwradii.dat (the ligand is simply made of C, N, O, H)</div>
<div>Yes, this is standard.</div>
<div>> ; Very approximate VanderWaals radii<br>> ; only used for drawing atoms as balls or for calculating atomic overlap.<br>> ; longest matches are used<br>> ; '???' or '*' matches any residue name<br>
> ; 'AAA' matches any protein residue name<br>> ??? C 0.15<br>> ??? F 0.12<br>> ??? H 0.04<br>> ??? N 0.110<br>> ??? O 0.105<br>> ??? S 0.16<br>><br>> My questions are<br>
> 1. anything wrong of my simulation procedures ?</div>
<div>In theory, not really. What values of potential energy and maximum force did<br>the energy minimization converge to?</div>
<div>> 2. how to find the clashed molecules ?<br>></div>
<div>Read the information printed to the log file (again, I'm assuming you're seeing<br>LINCS warnings, but you haven't told us what "broke" means!) and watch the<br>trajectory to see where things start to fall apart. As I suggested to someone<br>
earlier, if the crash is happening reasonably early, setting "nstxout = 1" is a<br>useful diagnostic to capture all frames prior to the crash.</div>
<div>-Justin</div>
<div>> Thank you<br>> Lin<br>><br>><br>><br>><br>><br>><br>></div>
<div>--<br>========================================</div>
<div>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080 (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></div>
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