<div>Hi Claire,<br><br></div><font color="#990099">-----gmx-users-bounces@gromacs.org wrote: -----<br><br></font><blockquote style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;">To: gmx-users@gromacs.org<br>From: Loison Claire <cloison@lasim.univ-lyon1.fr><br>Sent by: gmx-users-bounces@gromacs.org<br>Date: 11/03/2006 10:35AM<br>Subject: [gmx-users] QMMM gromacs/CPMD<br><br><font face="monospace" size="3">Dear gmx-users,<br><br>I would like to test the gromacs/CPMD combinaison for QMMM calculations.<br>For the system I am interested in, the configuration is "relatively <br>simple", the model contains<br>a single quantum solute molecule surrounded by classical solvent <br>molecules (water, let say).<br>So no broken bonds, and no dummy atoms. But it's complicated because <br>it's a liquid phase.<br><br>So i want to build the topology, including for example the "solute.itp" <br>file.<br>What puzzles me, is that i should give some information about a <br>classical force field<br>describing the atoms in my quantum solute... But i cannot set in advance <br>agood classical force field for it:<br>If I had, i would not bother about QMMM.<br><br></font><font face="monospace" size="3">pb> right. All you need to provide is the topology and any guess/garbage <br>parameter for the electrostatic and all bonded interactions. But you need <br>some consistent parameter for the Lennard-Jones since QM/MM Hamiltonian does <br>not couple the LJ interaction and they are evaluated in Gromacs.<br>
</font><br><font face="monospace" size="3"><br>So I have several questions about the gromacs/CPMD:<br>(1) does gromacs use at the force-field parameters concerning the <br>quantum atoms ?<br>When and for what ? How critical are those parameters ?<br><br></font><font face="monospace" size="3">pb> Only LJ interaction parameters between QM and MM atoms are important but<br>none of the others (ESP charge, and any bonded parameters).</font><br><font face="monospace" size="3"><br>(2) i think about building a quick and dirty approximate classical <br>force field for my solute molecule, in order to<br>create classically a starting point before doing the QMMM. But of course <br>as my force-field is probably bad,<br>the system may explode as soon as i change the model. So do you have <br>some advise how to construct my first system ?<br><br>pb> provide any value for the ESP charges and some 'good' guess for the LJ.<br>provide any values for the bond, angle dihedral, etc; they won't matter.<br><br>(3) an other question which is more CPMD related : i am now testing<br>the influence of size of the quantum bounding box<br>and the poisson solver on the electronic structure of my solute.<br>As i understood, this SYMMETRY 0 is in order to avoid<br>seeing the electrostatic periodic images which<br>are instrinsically present in plane-wave calculation.<br>In vacuum it's exactly what i want. But my QMMM system is a liquid, i <br>want to have periodic<br>boundary conditions for my MM box (the gromacs'one, not the CPMD one).<br>What does the QM system feel if i take the ususal pbc of gromacs input <br>? Does it see its<br>periodic images (I mean with the periodicity of the MM box ) ?<br><br><br>pb> No, QM won't see any periodic image of MM. it works with a Coulomb cut-off.<br>**I saw an uncorrected typo in the official version of CPMD-3.11.1 which is related <br></font><font face="monospace" size="3">to the consideration of QM/MM interaction from second and third layers (</font><font face="monospace" size="3">note: the MM atoms <br>are divided into 3 different layers for the QM so that simple approximations be made for<br>the distant water molecules. The typo won't affect you if you choose a QM/MM Coulomb cutoff <br>large enough so that the code includes all your MM atoms in the first MM layer <br>(look at your CPMD_inp.run).<br><br><br>Do i have to take care that the QM system does not cross the boundary of <br>the MM box ?<br><br>pb> No. For QM, the interface translates the atoms to the center of the QM box<br>and this translation is invissible to MM.<br><br>(4) in the examples from the Gogonea's group ( <br><a href="http://comppsi.csuohio.edu/groups/qmmm.html">http://comppsi.csuohio.edu/groups/qmmm.html</a>,<br>which i had difficulties to run, by the way), <br><br>pb> what sort of?<br><br>the gromacs cutoff for <br>the electrostatic interaction is set to 0.<br><br>pb> where? Anyway, the Gromacs electrostatic cutoff and QM/MM electroststic<br>cutoff are independent. So that, you can have PME for MM but your convenient<br>cutoff for QM; choice and consequences are yours.<br><br>Is that compulsory ?<br><br>pb> No.<br><br>cheers,<br>pb.<br><br></font><font face="monospace" size="3">Thanks for any suggestions and for your understanding about confused <br>questions..<br><br></font><font face="monospace" size="3">Claire Loison<br><br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></font>
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